Philippa Kaur

Hughes, T. P. et al. Global warming and recurrent mass bleaching of corals. Nature 543, 373–377 (2017).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Glynn, P. W. Coral reef bleaching: facts, hypotheses and implications. Glob. Chang. Biol. 2, 495–509 (1996).ADS 
Article 

Google Scholar 
Riegl, B. & Piller, W. E. Possible refugia for reefs in times of environmental stress. Int. J. Earth Sci. 92, 520–531 (2003).Article 

Google Scholar 
Hinderstein, L. M. et al. Theme section on ‘Mesophotic Coral Ecosystems: Characterization, Ecology, and Management’. Coral Reefs 29, 247–251 (2010).ADS 
Article 

Google Scholar 
Bongaerts, P., Ridgway, T., Sampayo, E. M. & Hoegh-Guldberg, O. Assessing the ‘deep reef refugia’ hypothesis: Focus on Caribbean reefs. Coral Reefs 29, 309–327 (2010).Article 

Google Scholar 
Smith, T. B. et al. Caribbean mesophotic coral ecosystems are unlikely climate change refugia. Global Change Biol. 22, 2756–2765 (2016).ADS 
Article 

Google Scholar 
Frade, P. R. et al. Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching. Nat. Commun. 9, 3447 (2018).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Holstein, D. M., Paris, C. B., Vaz, A. C. & Smith, T. B. Modeling vertical coral connectivity and mesophotic refugia. Coral Reefs 35, 23–37 (2016).ADS 
Article 

Google Scholar 
Prasetia, R., Sinniger, F., Hashizume, K. & Harii, S. Reproductive biology of the deep brooding coral Seriatopora hystrix: Implications for shallow reef recovery. PLoS ONE 12, e0177034 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Shlesinger, T., Grinblat, M., Rapuano, H., Amit, T. & Loya, Y. Can mesophotic reefs replenish shallow reefs? Reduced coral reproductive performance casts a doubt. Ecology 99, 421–437 (2018).PubMed 
Article 

Google Scholar 
Gleason, D. F. & Hofmann, D. K. Coral larvae: From gametes to recruits. J. Exp. Mar. Bio. Ecol. 408, 42–57 (2011).Article 

Google Scholar 
Hughes, T. P. & Tanner, J. E. Recruitment failure, life histories, and long-term decline of Caribbean corals. Ecology 81, 2250–2263 (2000).Article 

Google Scholar 
Bongaerts, P. et al. Deep reefs are not universal refuges: Reseeding potential varies among coral species. Sci. Adv. 3, e1602373 (2017).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
van Oppen, M. J. H., Bongaerts, P., Underwood, J. N., Peplow, L. M. & Cooper, T. F. The role of deep reefs in shallow reef recovery: An assessment of vertical connectivity in a brooding coral from west and east Australia. Mol. Ecol. 20, 1647–1660 (2011).PubMed 
Article 

Google Scholar 
Cohen, I. & Dubinsky, Z. Long term photoacclimation responses of the coral Stylophora pistillata to reciprocal deep to shallow transplantation: Photosynthesis and calcification. Front. Mar. Sci. 2, 45 (2015).Article 

Google Scholar 
Eyal, G. et al. Euphyllia paradivisa, a successful mesophotic coral in the northern Gulf of Eilat/Aqaba, Red Sea. Coral Reefs 35, 91–102 (2016).ADS 
Article 

Google Scholar 
Ben-Zvi, O. et al. Photophysiology of a mesophotic coral 3 years after transplantation to a shallow environment. Coral Reefs 39, 903–913 (2020).Article 

Google Scholar 
Murata, N., Takahashi, S., Nishiyama, Y. & Allakhverdiev, S. I. Photoinhibition of photosystem II under environmental stress. Biochim. Biophys. Acta Bioenerget. 1767, 414–421 (2007).CAS 
Article 

Google Scholar 
Takahashi, S. & Murata, N. How do environmental stresses accelerate photoinhibition?. Trends Plant Sci. 13, 178–182 (2008).CAS 
PubMed 
Article 

Google Scholar 
Cumbo, V. R., Baird, A. H. & van Oppen, M. J. H. The promiscuous larvae: Flexibility in the establishment of symbiosis in corals. Coral Reefs 32, 111–120 (2013).ADS 
Article 

Google Scholar 
Little, A. F., Van Oppen, M. J. H. & Willis, B. L. Flexibility in algal endosymbioses shapes growth in reef corals. Science 304, 1492–1494 (2004).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Sinniger, F., Morita, R. & Harii, S. ‘Locally extinct’ coral species Seriatopora hystrix found at upper mesophotic depths in Okinawa. Coral Reefs 32, 153 (2013).ADS 
Article 

Google Scholar 
Sinniger, F. et al. Overview of the mesophotic coral ecosystems around Sesoko Island, Okinawa, Japan. Galaxea J. Coral Reef Stud. 24, 69–76 (2022).Article 

Google Scholar 
Loya, Y. et al. Coral bleaching: the winners and the losers. Ecol. Lett. 4, 122–131 (2001).Article 

Google Scholar 
van Woesik, R., Sakai, K., Ganase, A. & Loya, Y. Revisiting the winners and the losers a decade after coral bleaching. Mar. Ecol. Prog. Ser. 434, 67–76 (2011).ADS 
Article 

Google Scholar 
Sinniger, F., Prasetia, R., Yorifuji, M., Bongaerts, P. & Harii, S. Seriatopora diversity preserved in upper mesophotic coral ecosystems in Southern Japan. Front. Mar. Sci. 4, 155 (2017).Article 

Google Scholar 
Atoda, K. The larva and postlarval development of some reef-building corals. V. Seriatopora hystrix. Sci. Rep. Tohoku Univ. 19, 33–39 (1951).
Google Scholar 
Hata, T. et al. Coral larvae are poor swimmers and require fine-scale reef structure to settle. Sci. Rep. 7, 2249 (2017).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Harii, S. & Kayanne, H. Larval dispersal, recruitment, and adult distribution of the brooding stony octocoral Heliopora coerulea on Ishigaki Island, southwest Japan. Coral Reefs 22, 188–196 (2003).Article 

Google Scholar 
Mulla, A. J., Lin, C. H., Takahashi, S. & Nozawa, Y. Photo-movement of coral larvae influences vertical positioning in the ocean. Coral Reefs 40, 1297–1306 (2021).Article 

Google Scholar 
Figueiredo, J., Baird, A. H., Harii, S. & Connolly, S. R. Increased local retention of reef coral larvae as a result of ocean warming. Nat. Clim. Chang. 4, 498–502 (2014).ADS 
Article 

Google Scholar 
Shanks, A. L., Largier, J., Brink, L., Brubaker, J. & Hooff, R. Demonstration of the onshore transport of larval invertebrates by the shoreward movement of an upwelling front. Limnol. Oceanogr. 45, 230–236 (2000).ADS 
Article 

Google Scholar 
Singh, T. et al. Long-term trends and seasonal variations in environmental conditions in Sesoko Island, Okinawa, Japan. Galaxea J. Coral Reef Stud. 24, 121–133 (2022).Article 

Google Scholar 
Roth, M. S., Fan, T.-Y. & Deheyn, D. D. Life history changes in coral fluorescence and the effects of light intensity on larval physiology and settlement in Seriatopora hystrix. PLoS ONE 8, e59476 (2013).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Mundy, C. N. & Babcock, R. C. Role of light intensity and spectral quality in coral settlement: Implications for depth-dependent settlement?. J. Exp. Mar. Bio. Ecol. 223, 235–255 (1998).Article 

Google Scholar 
Nesa, B., Baird, A. H., Harii, S., Yakovleva, I. & Hidaka, M. Algal symbionts increase DNA damage in coral planulae exposed to sunlight. Zool. Stud. 51, 12–17 (2012).CAS 

Google Scholar 
Cunning, R. & Baker, A. C. Excess algal symbionts increase the susceptibility of reef corals to bleaching. Nat. Clim. Change 3, 259–262 (2013).ADS 
Article 

Google Scholar 
Nakamura, T. Mass coral bleaching event in Sekisei lagoon observed in the summer of 2016. J. Jpn. Coral Reef Soc. 19, 29–40 (2017).Article 

Google Scholar 
Sakai, K., Singh, T. & Iguchi, A. Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016. PeerJ 7, e8138 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Edmunds, P. J., Gates, R. D. & Gleason, D. F. The biology of larvae from the reef coral Porites astreoides, and their response to temperature disturbances. Mar. Biol. 139, 981–989 (2001).Article 

Google Scholar 
Baker, A. C. Reef corals bleach to survive change. Nature 411, 765–766 (2001).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Bongaerts, P. et al. Adaptive divergence in a scleractinian coral: Physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats. BMC Evol. Biol. 11, 303 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Einbinder, S. et al. Novel adaptive photosynthetic characteristics of mesophotic symbiotic microalgae within the reef-building coral, Stylophora pistillata. Front. Mar. Sci. 3, 195 (2016).Article 

Google Scholar 
Rogers, C. S., Fitz, H. C., Gilnack, M., Beets, J. & Hardin, J. Scleractinian coral recruitment patterns at Salt River submarine canyon, St. Croix, U.S. Virgin Islands. Coral Reefs 3, 69–76 (1984).ADS 
Article 

Google Scholar 
Maida, M., Collb, J. C. & Sammarco, P. W. Shedding new light on scleractinian coral recruitment. J. Exp. Mar. Biol. Ecol. 180, 189–202 (1994).Article 

Google Scholar 
Sato, M. Mortality and growth of juvenile coral Pocillopora damicornis (Linnaeus). Coral Reefs 4, 27–33 (1985).ADS 
Article 

Google Scholar 
Nozawa, Y. Micro-crevice structure enhances coral spat survivorship. J. Exp. Mar. Biol. Ecol. 367, 127–130 (2008).Article 

Google Scholar 
Gleason, D. F. & Wellington, G. M. Ultraviolet radiation and coral bleaching. Nature 365, 836–838 (1993).ADS 
Article 

Google Scholar 
Shlesinger, T. & Loya, Y. Depth-dependent parental effects create invisible barriers to coral dispersal. Commun. Biol. 4, 1–10 (2021).Article 

Google Scholar 
Groves, S. H. et al. Growth rates of Porites astreoides and Orbicella franksi in mesophotic habitats surrounding St. Thomas, US Virgin Islands. Coral Reefs 37, 345–354 (2018).ADS 
Article 

Google Scholar 
Al-Horani, F. A., Al-Moghrabi, S. M. & De Beer, D. The mechanism of calcification and its relation to photosynthesis and respiration in the scleractinian coral Galaxea fascicularis. Mar. Biol. 142, 419–426 (2003).CAS 
Article 

Google Scholar 
Jiang, L. et al. Increased temperature mitigates the effects of ocean acidification on the calcification of juvenile Pocillopora damicornis, but at a cost. Coral Reefs 37, 71–79 (2018).ADS 
Article 

Google Scholar 
Jurriaans, S. & Hoogenboom, M. O. Thermal performance of scleractinian corals along a latitudinal gradient on the Great Barrier Reef. Philos. Trans. R. Soc. B Biol. Sci. 374, 20180546 (2019).CAS 
Article 

Google Scholar 
Brown, B. E. et al. Diurnal changes in photochemical efficiency and xanthophyll concentrations in shallow water reef corals: evidence for photoinhibition and photoprotection. Coral Reefs 18, 99–105 (1999).Article 

Google Scholar 
Salih, A., Larkum, A., Cox, G., Kühl, M. & Hoegh-Guldberg, O. Fluorescent pigments in corals are photoprotective. Nature 408, 850–853 (2000).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Matz, M. V., Marshall, N. J. & Vorobyev, M. Are corals colorful?. Photochem. Photobiol. 82, 345–350 (2006).CAS 
PubMed 
Article 

Google Scholar 
Haddock, S. H. D. & Dunn, C. W. Fluorescent proteins function as a prey attractant: Experimental evidence from the hydromedusa Olindias formosus and other marine organisms. Biol. Open 4, 1094–1104 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Eyal, G. et al. Spectral diversity and regulation of coral fluorescence in a mesophotic reef habitat in the Red Sea. PLoS ONE 10, 1–19 (2015).Article 
CAS 

Google Scholar 
Ben-Zvi, O., Eyal, G. & Loya, Y. Light-dependent fluorescence in the coral Galaxea fascicularis. Hydrobiologia 759, 15–26 (2015).Article 

Google Scholar 
Roth, M. et al. Fluorescent proteins in dominant mesophotic reef-building corals. Mar. Ecol. Prog. Ser. 521, 63–79 (2015).ADS 
CAS 
Article 

Google Scholar 
Ben-Zvi, O., Eyal, G. & Loya, Y. Response of fluorescence morphs of the mesophotic coral Euphyllia paradivisa to ultra-violet radiation. Sci. Rep. 9, 1–9 (2019).CAS 
Article 

Google Scholar 
Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Oliver, E. C. J. et al. Longer and more frequent marine heatwaves over the past century. Nat. Commun. 9, 1324 (2018).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Nakamura, T., van Woesik, R. & Yamasaki, H. Photoinhibition of photosynthesis is reduced by water flow in the reef-building coral Acropora digitifera. Mar. Ecol. Prog. Ser. 301, 109–118 (2005).ADS 
Article 

Google Scholar  More

Sophie Gilbert left a tenured position to join a start-up that allows small private landowners to sell carbon credits for preserving forests on their land.Credit: Sophie Gilbert

It was during a car journey to California in temperatures sometimes exceeding 40 °C that Sophie Gilbert decided she needed to make a major career change.Driving to visit family from her home in Moscow, Idaho, she passed columns of wildfire smoke, the oppressive heat limiting the time she could spend out of her air-conditioned car. The two-day drive midway through last year helped to crystallize a feeling that she urgently needed to do something more concrete to help deal with the threat of climate change.“It hit at a gut level,” says Gilbert. “Climate change isn’t something that’s going to happen to someone else later on. It felt deeply, viscerally real for me and my family and what I care about.”Given her role as a wildlife ecologist at the University of Idaho in Moscow, it might seem that Gilbert was already well placed to have a positive impact on climate change. But the slow, incremental pace of academia, and the difficulty of getting policymakers to act on her findings, left her feeling that she was not making as much of a difference as she’d hoped.“I’ve been studying how wildlife responds to environmental change to inform conservation planning for 15 years now, researching and publishing and waiting for something to happen and then having it not happen, even when I’ve worked closely with wildlife and land-management agencies,” she says. “The system just isn’t designed to respond to the urgent challenges we’re facing,” she says.Gilbert took stock of her skills and knowledge, and how they could be put to use, settling on nature-based solutions such as forest-carbon storage and biodiversity. She made a shortlist of companies and non-governmental organizations (NGOs) doing that kind of work and started contacting them to discuss her options.In April this year, a month after securing tenure, Gilbert joined Natural Capital Exchange, a start-up firm based in San Francisco, California. The company allows small private landowners to sell carbon credits for preserving forests on their land. Gilbert’s role as senior lead for natural capital involves adding biodiversity credits to the company’s offerings, to provide incentives for conserving functioning, well-managed forests.Giving up the security and freedom that tenure offers was a big step, but Gilbert says that the hardest part of the decision was actually breaking the news to her graduate students, whose reactions ranged from anger, to understanding, to some combination of the two. “There’s a lot of mentoring and mutual responsibility there, so telling them and helping them through the process of finding a new adviser has been by far the most emotionally gruelling part,” she says.But she is excited to be taking up the challenge of working in the fast-paced world of a start-up company. “The company is full of rigorous, smart people who want to do good work,” she says. “It’s going to be a wild and exciting ride.”Spreading the wordIt’s a ride that Alice Bell knows well. By 2015, she had spent 11 years working as a lecturer in science communication at Imperial College London, and as a research fellow in the Science Policy Research Unit at the University of Sussex in Brighton, UK. She decided to leave academia for good and took up a position as head of communications at the climate-change campaign group Possible, based in London.The move came about partly by necessity — Bell’s contract was due to end, and she felt that UK government cuts were making academia an ever-more precarious occupation — but it stemmed mainly from a desire to be more directly involved in tackling the climate crisis.While at Imperial, she had built and launched a college-wide interdisciplinary course on climate change that had forced her to look more deeply into the issue. “I felt a greater urgency to put my skills somewhere they would be best utilized,” she says.Bell says leaving academia was the right choice. She thinks she is having a bigger impact on the climate crisis, and that her work–life balance has improved; she also feels more engaged in her work. “I feel more intellectually stimulated in workshops with NGOs than I did in most academic meetings,” she says, adding that she finds it liberating to be freed from academia’s pressure to publish, and from the weight of that pressure on career progression.But there are some drawbacks. “When you’re working for a small charity, no one knows who you are,” says Bell. “I was taken more seriously when I could say I was from Imperial.”Some might fear that leaving academia could arouse suspicions that they weren’t good enough to stay. “Ignore that voice,” she advises. “For many individuals, it could well be the best decision to give up.”Change from withinNot everyone, however, is ready or willing to give up on an academic career that they have spend years building up. And some find opportunities to get more involved in concrete climate solutions from within academia.

Meade Krosby provides natural-resource managers and policymakers with scientific evidence on climate-change impacts and adaptation actions.Credit: Eric Bruns

Since 2017, Meade Krosby has combined an academic post as a senior scientist at the University of Washington’s Climate Impacts Group in Seattle, where she works on climate vulnerability assessment and adaptation planning, with a director’s role at the university’s Northwest Climate Adaptation Science Center. The centre provides natural-resource managers and policymakers in the region with scientific evidence on climate-change impacts and adaptation actions. Krosby calls it a “boundary organization”, an interface between science and society, “acting as a conduit between the two”.“We bring applied science to decision-making around climate change, and bring decision-makers’ and communities’ concerns and knowledge back into academia to inform the kind of research that is done,” she says.Between 2016 and 2018, Krosby collaborated with Indigenous scholars, tribal organizations and other university scientists to develop the Tribal Climate Tool, a free online resource that aims to get the best available climate projections into the hands of Indigenous communities, to inform their planning for climate change. The tool, which launched in 2018, is now being used in many hazard-mitigation plans, such as the Samish Indian Nation’s 2019 climate-change vulnerability assessment. Krosby is also writing a paper on its development and use, producing a more conventional academic output to complement a tool that makes a difference in the real world.“You can do really useful work that doesn’t look like basic science, but it’s not always a trade-off between doing cool science and useful science,” she says.Funding challengeKrosby knew early on in her academic career that she wanted to make practical contributions that would help society to prepare for climate change. She started looking for this kind of applied work in 2009, during her postdoctoral research at the University of Washington, but found it hard at first to find funding — either from federal funding agencies or from private foundations. Then, in 2010, she received funding from the US Department of the Interior to look at species mobility and connectivity, and was able to use that to create a position for herself in the Climate Impacts Group.But she quickly found that her experience in more conventional academic settings had not prepared her for the kinds of project that the group undertook, with the aim of making science useful for policymakers and the public. “It was shocking how ill-prepared I was for transdisciplinary work,” she says. “We’re not trained to do, or to value, those kinds of collaborations.” The centre now supports fellowships and training in societally engaged research, and Krosby teaches a graduate course on how to connect science to society. “It’s an opportunity to train early-career scientists to do the work we never got trained to do,” she says. In 2020, she co-authored a paper1 calling for changes in how scientists are trained, by emphasizing skills such as collaboration and communication1.Academic career structures are not set up to promote and reward work that requires lots of collaboration with people outside the university, and which doesn’t necessarily result in a typical scientific publication, says Krosby. “The work I want to do wouldn’t be rewarded in a tenure-track position,” she adds. “To do this effectively, universities need to think about their incentive structure. Is a peer-reviewed paper really the most important outcome?”Reef encounterJulia Baum, a marine ecologist at the University of Victoria in Canada, has found a way to do practical, climate-focused work in a standard academic job. For her, the turning point came in 2015, when a massive marine heatwave nearly wiped out the tropical reef she was studying. “I watched a beautiful pristine reef melt down in 10 months,” she says. “I used to think overfishing was the biggest threat — then climate change came and hit me over the head.”

Julia Baum records data on the Pacific atoll of Kiritimati, after a marine heatwave in 2015 nearly destroyed the coral reef.Credit: Kristina Tietjen

That experience prompted her to completely overhaul her research programme to focus exclusively on climate impacts and how to mitigate them. “I want to do more than just document a sinking ship — I want to help right it,” she says.Baum’s tenured position offers her the flexibility of making that change, and she says she felt a moral obligation to apply her knowledge in a way that would help address the biggest threat facing the planet. As well as redirecting her research, Baum is designing a cross-university graduate-training programme focused on coastal climate solutions. This will offer training in professional skills that are crucial for climate work but are rarely taught in universities — such as how to collaborate and negotiate with non-academic partners, and how to deal with the media.But, like Krosby, Baum says she and many of her colleagues feel frustrated that a lot of universities don’t seem to value or support any kind of work outside conventional academic publications. Those who want to apply their findings to real-world problems often have to do it on their own, with no real benefit to their academic career. “Universities need to rise to the challenge and find innovative ways to support their faculty, by valuing and rewarding solutions work in their hiring and promotion criteria,” she says.If they don’t, universities risk losing more dedicated researchers such as Gilbert and Bell to the private sector. “If there comes a point when the climate-solutions impact I can have within academia seems too small, then yes, I would make the leap,” says Baum.Maximum impactFor academics looking for a way to take on a bigger role in the fight against climate change, there are a lot of options — from finding or making your own position in a university, to leaving for a company or charity that is doing more immediate, hands-on work. But the first step is working out where you can have the most impact, and what you can bring to the table. “For many people, the biggest impact you can have is through your students,” says Gilbert. “If you can focus on that and feel satisfied, that’s great.”For those who choose to leave, however, it pays to spend some time doing your research, finding companies and organizations that are doing the kind of work you are interested in, and talking to them about what you could offer. You might be surprised to find just how useful your skills can be outside academia — not just the disciplinary knowledge you have gained, but transferable skills such as technical writing and the ability to review and synthesize complex research. “The list of things we’re good at is pretty awesome,” says Gilbert. More

Authors and AffiliationsSmithsonian Tropical Research Institute – STRI, Balboa, Republic of PanamaGustavo A. Castellanos-Galindo, D. Ross Robertson, Diana M. T. Sharpe & Mark E. TorchinLeibniz Centre for Tropical Marine Research (ZMT), Bremen, GermanyGustavo A. Castellanos-GalindoAuthorsGustavo A. Castellanos-GalindoD. Ross RobertsonDiana M. T. SharpeMark E. TorchinCorresponding authorCorrespondence to
Gustavo A. Castellanos-Galindo. More

Dauvin, J. C. et al. The well sorted fine sand community from the western Mediterranean Sea: A resistant and resilient marine habitat under diverse human pressures. Environ. Pollut. 224, 336–351 (2017).CAS 
PubMed 
Article 

Google Scholar 
Obolewski, K. & Glińska-Lewczuk, K. Connectivity and complexity of coastal lakes as determinants for their restoration-A case study of the southern Baltic Sea. Ecol. Eng. 155, 1700 (2020).Article 

Google Scholar 
Dobrowolski, Z. Occurrence of macrobenthos in different littoral habitats of the polymictic Lebsko lake. Ekologia Polska 42, 19–40 (1994).
Google Scholar 
Paturej, E., Gutkowska, A. & Durczak, K. Biodiversity and indicative role of zooplankton in the shallow macrophyte-dominated lake Łuknajno. Pol. J. Nat. Sci. 27, 53–66 (2012).
Google Scholar 
Obolewski, K. et al. Patterns of salinity regime in coastal lakes based on structure of benthic invertebrates. PLoS ONE 13, 150 (2018).Article 
CAS 

Google Scholar 
Lew, S., Glińska-Lewczuk, K. & Lew, M. The effects of environmental parameters on the microbial activity in peat-bog lakes. PLoS ONE 14, 179 (2019).
Google Scholar 
Bremner, J. Species’ traits and ecological functioning in marine conservation and management. J. Exp. Mar. Biol. Ecol. 366, 37–47 (2008).Article 

Google Scholar 
Törnroos, A. & Bonsdorff, E. Developing the multitrait concept for functional diversity: Lessons from a system rich in functions but poor in species. Ecol. Appl. 22, 2221–2236 (2012).PubMed 
Article 

Google Scholar 
Baldrighi, E. & Manini, E. Deep-sea meiofauna and macrofauna diversity and functional diversity: are they related?. Mar. Biodivers. 45, 469–488 (2015).Article 

Google Scholar 
Belley, R. & Snelgrove, P. V. R. Relative contributions of biodiversity and environment to benthic ecosystem functioning. Front. Mar. Sci. 3, 7598 (2016).Article 

Google Scholar 
Díaz, S. & Cabido, M. Vive la différence: Plant functional diversity matters to ecosystem processes. Trends Ecol. Evol. 16, 646–655 (2001).Article 

Google Scholar 
Gagic, V. et al. Functional identity and diversity of animals predict ecosystem functioning better than species-based indices. Proc. R. Soc. B Biol. Sci. 282, 689 (2015).
Google Scholar 
Ding, N. et al. Different responses of functional traits and diversity of stream macroinvertebrates to environmental and spatial factors in the Xishuangbanna watershed of the upper Mekong River Basin, China. Sci. Total Environ. 574, 288–299 (2017).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Kenny, A. J. et al. Assessing cumulative human activities, pressures, and impacts on North Sea benthic habitats using a biological traits approach. ICES J. Mar. Sci. 75, 1080–1092 (2018).Article 

Google Scholar 
Llanos, E. N., Saracho Bottero, M. A., Jaubet, M. L., Elías, R. & Garaffo, G. V. Functional diversity in the intertidal macrobenthic community at sewage-affected shores from Southwestern Atlantic. Mar. Pollut. Bull. 157, 7448 (2020).Article 
CAS 

Google Scholar 
Paganelli, D., Marchini, A. & Occhipinti-Ambrogi, A. Functional structure of marine benthic assemblages using Biological Traits Analysis (BTA): A study along the Emilia-Romagna coastline (Italy, North-West Adriatic Sea). Estuar. Coast. Shelf Sci. 96, 245–256 (2012).ADS 
Article 

Google Scholar 
Nasi, F. et al. Functional biodiversity of marine soft-sediment polychaetes from two Mediterranean coastal areas in relation to environmental stress. Mar. Environ. Res. 137, 121–132 (2018).CAS 
PubMed 
Article 

Google Scholar 
Harwell, M. A. et al. Conceptual framework for assessing ecosystem health. Integr. Environ. Assess. Manag. 15, 544–564 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Hu, C. et al. Macrobenthos functional trait responses to heavy metal pollution gradients in a temperate lagoon. Environ. Pollut. 253, 1107–1116 (2019).CAS 
PubMed 
Article 

Google Scholar 
Ramsay, K., Kaiser, M. J. & Hughes, R. N. Responses of benthic scavengers to fishing disturbance by towed gears in different habitats. J. Exp. Mar. Biol. Ecol. 224, 4458 (1998).Article 

Google Scholar 
Sigala, K., Reizopoulou, S., Basset, A. & Nicolaidou, A. Functional diversity in three Mediterranean transitional water ecosystems. Estuar. Coast. Shelf Sci. 110, 202–209 (2012).ADS 
Article 

Google Scholar 
de Loiola, P. P., Cianciaruso, M. V., Silva, I. A. & Batalha, M. A. Functional diversity of herbaceous species under different fire frequencies in Brazilian savannas. Flora Morphol. Distrib. Funct. Ecol. Plants 205, 674–681 (2010).Article 

Google Scholar 
Schleuter, D., Daufresne, M., Massol, F. & Argillier, C. A user’s guide to functional diversity indices. Ecological Monographs vol. 80 http://www.scopus.com/scopus/search/form.urli (2010).Wan, H. W. M. R., Cooper, K. M., Froján, C. R. S. B., Defew, E. C. & Paterson, D. M. Impacts of physical disturbance on the recovery of a macrofaunal community: A comparative analysis using traditional and novel approaches. Ecol. Indicators 12, 37–45 (2012).Article 

Google Scholar 
Millet, B. & Guelorget, O. Spatial and seasonal variability in the relationships between benthic communities and physical environment in a lagoon ecosystem. Mar. Ecol. Prog. Ser. 108, 161–174 (1994).ADS 
Article 

Google Scholar 
McLusky, D. S. & Elliott, M. The Estuarine Ecosystem (Oxford University Press, 2004). https://doi.org/10.1093/acprof:oso/9780198525080.001.0001.Book 

Google Scholar 
Mrozińska, N. & Bąkowska, M. Effects of heavy metals in lake water and sediments on bottom invertebrates inhabiting the brackish coastal lake Łebsko on the southern baltic coast. Int. J. Environ. Res. Public Health 17, 1–19 (2020).Article 
CAS 

Google Scholar 
Petchey, O. L. & Gaston, K. J. Functional diversity: Back to basics and looking forward. Ecol. Lett. 9, 741–758 (2006).PubMed 
Article 

Google Scholar 
Villéger, S., Miranda, J. R., Hernández, D. F. & Mouillot, D. Contrasting changes in taxonomic vs. functional diversity of tropical fish communities after habitat degradation. Ecol. Appl. 20, 1512–1522 (2010).PubMed 
Article 

Google Scholar 
Dolédec, S. & Statzner, B. Theoretical habitat templets, species traits, and species richness: 548 plant and animal species in the Upper Rhône River and its floodplain. Freshw. Biol. 31, 523–538 (1994).Article 

Google Scholar 
Usseglio-Polatera, P., Bournaud, M., Richoux, P. & Tachet, H. Biomonitoring through biological traits of benthic macroinvertebrates: How to use species trait databases?. Hydrobiologia 422, 153–162 (2000).Article 

Google Scholar 
Charvet, S., Statzner, B., Usseglio-Polatera, P. & Dumont, B. Traits of benthic macroinvertebrates in semi-natural French streams: An initial application to biomonitoring in Europe. Freshw. Biol. 43, 277–296 (2000).Article 

Google Scholar 
Statzner, B., Dolédec, S. & Hugueny, B. Biological trait composition of European stream invertebrate communities: Assessing the effects of various trait filter types. Ecography 27, 470–488 (2004).Article 

Google Scholar 
Bremner, J., Rogers, S. I. & Frid, C. L. J. Assessing functional diversity in marine benthic ecosystems: A comparison of approaches. Mar Ecol Prog Ser 254, 5589 (2003).Article 

Google Scholar 
Tillin, H., Hiddink, J., Jennings, S. & Kaiser, M. Chronic bottom trawling alters the functional composition of benthic invertebrate communities on a sea-basin scale. Mar. Ecol. Prog. Ser. 318, 31–45 (2006).ADS 
Article 

Google Scholar 
Marchini, A., Munari, C. & Mistri, M. Functions and ecological status of eight Italian lagoons examined using biological traits analysis (BTA). Mar. Pollut. Bull. 56, 1076–1085 (2008).CAS 
PubMed 
Article 

Google Scholar 
Boikova, E., Botva, U. & Līcīte, V. Implementation of trophic status index in brackish water quality assessment of baltic coastal waters. Proc. Latv. Acad. Sci. Sect. B 62, 115–119 (2008).CAS 

Google Scholar 
Wielgat-Rychert, M., Jarosiewicz, A., Ficek, D., Pawlik, M. & Rychert, K. Nutrient fluxes and their impact on the phytoplankton in a Shallow Coastal Lake. Polish J. Environ. Stud. 24, 7780 (2015).Article 
CAS 

Google Scholar 
Kruk, C., Devercelli, M. & Huszar, V. L. Reynolds Functional Groups: A trait-based pathway from patterns to predictions. Hydrobiologia 848, 113–129 (2021).Article 

Google Scholar 
Trojanowski, J., Trojanowska, C. & Korzeniewski, K. Trophic state of coastal lakes. Polish Arch. Hydrobiol. 38, 23–34 (1975).
Google Scholar 
Astel, A. M., Bigus, K., Obolewski, K. & Glińska-Lewczuk, K. Spatiotemporal assessment of water chemistry in intermittently open/closed coastal lakes of Southern Baltic. Estuar. Coast. Shelf Sci. 182, 47–59 (2016).ADS 
CAS 
Article 

Google Scholar 
Choiński, A. Changes in morphometrics of the coastal lakes. in Hydroecological Determinants of Functioning of Southern Baltic Coastal Lakes (eds. Obolewski, K., Astel, A. & Kujawa, R.) 26–37 (PWN, 2017).Obolewski, K., Glińska-Lewczuk, K., Bąkowska, M., Szymańska, M. & Mrozińska, N. Patterns of phytoplankton composition in coastal lakes differed by connectivity with the Baltic Sea. Sci. Total Environ. 631–632, 951–961 (2018).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Szymańska-Walkiewicz, M., Glińska-Lewczuk, K., Burandt, P. & Obolewski, K. Phytoplankton sensitivity to heavy metals in Baltic Coastal Lakes. Int. J. Environ. Res. Public Health 19, 4131 (2022).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Mrozińska, N., Glińska-Lewczuk, K. & Obolewski, K. Salinity as a key factor on the benthic fauna diversity in the coastal lakes. Animals 11, 7440 (2021).Article 

Google Scholar 
Bremner, J., Rogers, S. I. & Frid, C. L. J. Methods for describing ecological functioning of marine benthic assemblages using biological traits analysis (BTA). Ecol. Ind. 6, 609–622 (2006).Article 

Google Scholar 
Papageorgiou, N., Sigala, K. & Karakassis, I. Changes of macrofaunal functional composition at sedimentary habitats in the vicinity of fish farms. Estuar. Coast. Shelf Sci. 83, 561–568 (2009).ADS 
CAS 
Article 

Google Scholar 
Lam-Gordillo, O., Baring, R. & Dittmann, S. Ecosystem functioning and functional approaches on marine macrobenthic fauna: A research synthesis towards a global consensus. Ecol Indic 115, 5589 (2020).Article 

Google Scholar 
Kołodziejczyk, A. & Koperski, P. Bezkręgowce słodkowodne Polski: klucz do oznaczania oraz podstawy biologii i ekologii makrofauny. (Wydawnictwa Uniwersytetu Warszawskiego, 2000).Wiederholm, Torgny. Chironomidae of the Holarctic Region: Keys and Diagnoses. Part 1: larvae. (1983).Antsulevich, A. et al. Helcom, 2012. Development of a set of core indicators: Interim report of the HELCOM CORESET project. PART A. Description of the selection process. (2012).Piechocki, A. & Wawrzyniak-Wydrowska, B. Guide to Freshwater and Marine Mollusca of Poland. (2016).Zettler, M. L. et al. Biodiversity gradient in the Baltic Sea: A comprehensive inventory of macrozoobenthos data. Helgol. Mar. Res. 68, 49–57 (2014).ADS 
Article 

Google Scholar 
Palomares, M. L. D. & Pauly, D. SeaLifeBase. https://www.sealifebase.ca/ (2021).MarLIN. BIOTIC-biological traits information catalogue. Marine Life Information Network. Plymouth: Marine Biological Association of the UK. http://www.marlin.ac.uk/biotic/ (2006).Horton, T. et al. World Register of Marine Species (WoRMS). https://www.marinespecies.org (2021).Chevene, F., Doleadec, S. & Chessel, D. A fuzzy coding approach for the analysis of long-term ecological data. Freshw. Biol. 31, 295–309 (1994).Article 

Google Scholar 
Oug, E., Fleddum, A., Rygg, B. & Olsgard, F. Biological traits analyses in the study of pollution gradients and ecological functioning of marine soft bottom species assemblages in a fjord ecosystem. J. Exp. Mar. Biol. Ecol. 432–433, 94–105 (2012).Article 

Google Scholar 
Egres, A. G., Hatje, V., Miranda, D. A., Gallucci, F. & Barros, F. Functional response of tropical estuarine benthic assemblages to perturbation by Polycyclic Aromatic Hydrocarbons. Ecol. Ind. 96, 229–240 (2019).CAS 
Article 

Google Scholar 
Charvet, S., Kosmala, A. & Statzner, B. Biomonitoring through biological traits of benthic macroinvertebrates: Perspectives for a general tool in stream management. Fundam. Appl. Limnol. 142, 415–432 (1998).Article 

Google Scholar 
Clarke, K. R. & Gorley, R. N. PRIMER v6: User Manual/Tutorial. (2006).Dobrowolski, Z. Density, biomass, and distribution of benthic invertebrates in the mid-lake zone of the coastal Lake Gardno. Oceanol. Stud. 30, 39–58 (2001).
Google Scholar 
Michaud, E., Desrosiers, G., Mermillod-Blondin, F., Sundby, B. & Stora, G. The functional group approach to bioturbation: II. The effects of the Macoma balthica community on fluxes of nutrients and dissolved organic carbon across the sediment-water interface. J. Exp. Mar. Biol. Ecol. 337, 178–189 (2006).CAS 
Article 

Google Scholar 
Taurusman, A. A. Community structure of macrozoobenthic feeding guilds in responses to eutrophication in Jakarta Bay. Biodivers. J. Biol. Divers. 11, 998 (2010).Article 

Google Scholar 
Uwadiae, R. E. Macroinvertebrates functional feeding groups as indices of biological assessment in a tropical aquatic ecosystem: implications for ecosystem functions. New York Sci. J. 3, 778 (2010).
Google Scholar 
Obolewski, K., Glińska-Lewczuk, K., Sidoruk, M. & Szymańska, M. M. Response of benthic fauna to habitat heterogeneity in a shallow temperate lake. Animals 11, 558 (2021).Article 

Google Scholar 
Rhoads, D. C. Organism-sediment relations on the muddy sea floor. in Oceanography and Marine Biology: An Annual Review. vol. 12 263–300 (Aberdeen University Press/Allen & Unwin, 1974).Thrush, S. F., Hewitt, J. E., Gibbs, M., Lundquist, C. & Norkko, A. Functional role of large organisms in intertidal communities: Community effects and ecosystem function. Ecosystems 9, 1029–1040 (2006).Article 

Google Scholar 
Frid, C. L. J., Harwood, K. G., Hall, S. J. & Hall, J. A. Long-term changes in the benthic communities on North Sea fishing grounds. in ICES Journal of Marine Science vol. 57 1303–1309 (Academic Press, 2000).Bradshaw, C., Veale, L. O. & Brand, A. R. The role of scallop-dredge disturbance in long-term changes in Irish Sea benthic communities: A re-analysis of an historical dataset. J. Sea Res. 47, 161–184 (2002).ADS 
Article 

Google Scholar 
Cañedo-Argüelles, M. et al. Can salinity trigger cascade effects on streams? A mesocosm approach. Sci. Total Environ. 540, 3–10 (2016).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Herbst, D. B. Salinity controls on trophic interactions among invertebrates and algae of solar evaporation ponds in the Mojave Desert and relation to shorebird foraging and selenium risk. Wetlands 26, 475–485 (2006).Article 

Google Scholar 
Merritt, R. W. et al. Development and application of a macroinvertebrate functional-group approach in the bioassessment of remnant river oxbows in southwest Florida. Am. Benthol. Soc. 21, 550 (2002).Article 

Google Scholar 
de Roos, A. M., Persson, L. & McCauley, E. The influence of size-dependent life-history traits on the structure and dynamics of populations and communities. Ecol. Lett. 6, 473–487 (2003).Article 

Google Scholar 
Reizopoulou, S. & Nicolaidou, A. Index of size distribution (ISD): A method of quality assessment for coastal lagoons. Hydrobiologia 577, 141–149 (2007).Article 

Google Scholar 
Basset, A., Pinna, M., Sabetta, L., Barbone, E. & Galuppo, N. Hierarchical scaling of biodiversity in lagoon ecosystems. Trans. Waters Bull. 2, 75–86 (2008).
Google Scholar 
Basset, A. et al. A benthic macroinvertebrate size spectra index for implementing the Water Framework Directive in coastal lagoons in Mediterranean and Black Sea ecoregions. Ecol. Ind. 12, 72–83 (2012).Article 

Google Scholar 
Robson, B. J., Barmuta, L. A. & Fairweather, P. G. Methodological and conceptual issues in the search for a relationship between animal body-size distributions and benthic habitat architecture. Mar. Freshw. Res. 56, 1–11 (2005).Article 

Google Scholar 
Parry, D. M., Kendall, M. A., Rowden, A. A. & Widdicombe, S. Species body size distribution patterns of marine benthic macrofauna assemblages from contrasting sediment types. J. Mar. Biol. Assoc. U.K. 79, 793–801 (1999).Article 

Google Scholar 
Netto, S. A., Domingos, A. M. & Kurtz, M. N. Effects of artificial breaching of a temporarily open/closed estuary on benthic macroinvertebrates (Camacho Lagoon, Southern Brazil). Estuaries Coasts 35, 1069–1081 (2012).CAS 
Article 

Google Scholar 
Folke, C. et al. Regime shifts, resilience, and biodiversity in ecosystem management. Annu. Rev. Ecol. Evol. Syst. 35, 557–581 (2004).Article 

Google Scholar 
Montefalcone, M., Parravicini, V. & Bianchi, C. N. Quantification of Coastal Ecosystem Resilience. in Treatise on Estuarine and Coastal Science 49–70 (Elsevier, 2011). https://doi.org/10.1016/B978-0-12-374711-2.01003-2.Sasaki, T., Furukawa, T., Iwasaki, Y., Seto, M. & Mori, A. S. Perspectives for ecosystem management based on ecosystem resilience and ecological thresholds against multiple and stochastic disturbances. Ecol. Ind. 57, 395–408 (2015).Article 

Google Scholar 
Smee, D. L., Reustle, J. W., Belgrad, B. A. & Pettis, E. L. Storms promote ecosystem resilience by alleviating fishing. Curr. Biol. 30, R869–R870 (2020).CAS 
PubMed 
Article 

Google Scholar 
Gilby, B. L. et al. Umbrellas can work under water: Using threatened species as indicator and management surrogates can improve coastal conservation. Estuar. Coast. Shelf Sci. 199, 132–140 (2017).ADS 
Article 

Google Scholar 
Henderson, C. J. et al. Landscape transformation alters functional diversity in coastal seascapes. Ecography 43, 138–148 (2020).Article 

Google Scholar 
Yeager, L. A., Geyer, J. K. & Fodrie, F. J. Trait sensitivities to seagrass fragmentation across spatial scales shape benthic community structure. J. Anim. Ecol. 88, 1743–1754 (2019).PubMed 
Article 

Google Scholar 
Darr, A., Gogina, M. & Zettler, M. L. Functional changes in benthic communities along a salinity gradient- a western Baltic case study. J. Sea Res. 85, 315–324 (2014).ADS 
Article 

Google Scholar 
Statzner, B., Bady, P., Dolédec, S. & Schöll, F. Invertebrate traits for the biomonitoring of large European rivers: An initial assessment of trait patterns in least impacted river reaches. Freshw. Biol. 50, 2136–2161 (2005).Article 

Google Scholar  More

Ethical statementEthics approval was obtained for this study from the ethics committee of the University of Goettingen (Chair: Prof. Dr. Peter-Tobias Stoll) under the reference number 17./04.22Wurz.Study areaAll plots were situated in northeastern Madagascar in the SAVA region (Supplementary Fig. 1). The natural vegetation is tropical lowland rainforest, but deforestation rates are high30,67.The region is globally and nationally one of the most biodiverse places with high levels of endemism17,68. Forest loss is mainly driven by slash-and-burn shifting hill rice cultivation58. The region is characterized by a warm and humid climate with an annual rainfall of 2255 mm and a mean annual temperature of 23,9 °C (mean value of 60 plots extracted from CHELSA climatology69). Vanilla is the main cash crop in the SAVA region, making Madagascar the main vanilla producer globally21,22. Vanilla prices have shown strong fluctuations over the past years, with a price boom between 2014 and 2019 triggering an expansion of vanilla agroforestry in the region22,23.Study designWe selected 10 villages based on the 60 villages selected within the Diversity Turn in Land Use Science project22 (Supplementary Fig. 1). We selected the villages based on the list of villages for our study region from official election lists which listed all villages within a fokontany individually22. Village boundaries, demographics, infrastructure were defined based on a rapid survey with the village chief. Among the 60 villages, we considered all villages without coconut plantations, with less than 40% water (river, sea, and lakes) to avoid a strong influence of water elements and with forest fragments and shifting cultivation present within a 2 km radius around the village. Two of these 17 villages overlapped within a 2 km radius of the villages, thus we randomly selected one of them, resulting in 14 villages. We visited these 14 villages in a randomized order and stopped after we found 10 villages which fulfilled the necessary criteria (all land-use types present, willing to participate). In each of the 10 villages, we selected three vanilla agroforests, one forest fragment, and two fallows. Overall, we studied 60 plots across 10 villages and 10 plots in one protected old-growth forest (Marojejy National Park). All plots had a minimum distance of 260 m and a mean minimum distance of 794 m (SD = 468 m) to each other. Plot elevation ranged between 10 and 819 m.a.s.l. (mean  = 205 m, SD = 213 m; Supplementary Table 20).Plot selectionIn each of the 10 villages, we selected three vanilla agroforests with low, medium, and high canopy closure, respectively, covering a within village canopy cover gradient. To refine our vanilla agroforest classification, we used interviews with the plot owners to categorize all vanilla agroforests based on land-use history into fallow- and forest-derived agroforests15. Forest-derived vanilla agroforests are established within forest fragments, which have been manually thinned of dense understory vegetation. Fallow-derived vanilla agroforests are established on formerly slashed and burned plots, where vegetation has been cleared for hill rice production (shifting cultivation system locally called tavy). Out of our 30 vanilla agroforests, 20 vanilla agroforests were fallow-derived and 10 vanilla agroforests were forest-derived, roughly matching the proportion of fallow- and forest-derived vanilla agroforests across the study region (70% are fallow-derived vanilla agroforests, 27% are forest-derived vanilla agroforests and 3% of unknown origin22.In addition to vanilla agroforests, we selected one forest fragment in each village. Forest fragments were located inside the agricultural landscape and were remnants of the once continuous forest; these fragments are frequently used for natural product extraction. Forest fragments have not been burned or clear cut in living memory, yet the ongoing resource extraction results in a much simplified stand structure and fewer large trees compared to old-growth forest12. Furthermore, we chose one herbaceous and one woody fallow in each of the 10 study villages. Both fallow types form part of the shifting hill rice production cycle and represent the fallow period at different stages after the crop production. Herbaceous fallows have been slashed and burned multiple times with the last cultivation cycle at the end of 2016, one year prior to the first species data collection in 2017, and thereafter left fallow11. The continuous succession of herbaceous fallows turns them into woody fallows with the domination of woody plants including shrubs, trees, and sometimes bamboo. Our 10 woody fallows have last burned 4–16 years before data collection. In this study, we combine both herbaceous and woody fallows into the category “fallow”. Generally, fallows occur in different forms in the study region. The characteristics of fallows depend on the frequency of past fires and the length of fallow periods in between crop cultivation11. Frequent burning results in a loss of native and woody species and a dominance of exotic species and grasses11. In later fallow cycles, fern species increasingly appear11.Due to the commonly repeated slashing and burning, secondary forests are very rare in the study region. Shifting cultivation prevails in Madagascar70, because it is an important option for people to grow food because means for agricultural intensification are scarce. According to our baseline survey (performed in 60 villages in our study region), 90% of the interviewed farmers grow rice for subsistence in addition to growing vanilla22. Out of this sample, 64% of farmers grow rice in irrigated paddies and 26% of farmers use shifting cultivation.We also studied 10 plots at two sites in Marojejy National Park, the only remaining, continuous old-growth forest at a low altitude in our study area71. We chose accessible old-growth forest plots with a minimum distance of 250 m from the forest edge. Five of the 10 old-growth forest plots were located in Manantenina Valley, the other five old-growth forest plots were situated in the eastern part of Marojejy National Park, called Bangoabe area. Illegal selective logging has occurred in some parts of the park. During our plot selection, we avoided sites with traces of selective logging.Land-use history classificationTo collect information on the land-use history or farm history, interviews with farmers are common72,73. We did interviews with the plot owner. Questions on land-use history were binary (forest-derived or fallow-derived) and did not include information on the detailed land-use history (e.g. frequency of burning, past crop systems). Thus, we consider this selfreported data very reliable. The land-use categorization derived by farmers was confirmed by our visual plot inspections (forest-derived vanilla agroforests do have a quite distinctive vegetation structure compared to fallow-derived vanilla agroforests). Additionally, data on tree species composition and soil characteristics show evident differences between the categories and back up the binary land-use history categorization. Analysis of tree species composition showed that fallow- and forest-derived vanilla agroforests differ significantly in tree species composition12. Soil analysis (see Fig. S9) showed that our fallow-derived vanilla agroforests are associated with fertility-related variables such as an increase in calcium, pH, nitrogen, and phosphorus, which is common after slas-and-burn agriculture74,75.Plot designWe collected species data on plots with a radius of 25 m (1964 m2, 0.1964 ha). We established our circular plots in a homogeneous area of the land-use type or forest. Adjacent land uses were usually different because farmers generally own small-scale land with a mean size of 0.66 ha (mean size of agroforests). We assessed vanilla plant data (yield, vine length, vine age, planting density) on 36 vanilla pieds on each of 30 circular vanilla plots (Supplementary Fig. 8). We defined one vanilla pied (foot in French) as the combination of a vanilla vine and a minimum of one support tree. The 36 vanilla pieds were evenly selected in each of the circular plots based on a sampling protocol to ensure comprehensive and unbiased sampling. We chose vanilla pieds independent of age, length or health condition. We marked the 36 selected vanilla pieds per plot with a unique barcode to assess vanilla yield (April 2018) and other plant health variables on the same plant (not used in this study). However, for 37 vanilla pieds (out of a total of 1080 marked vanilla pieds), the barcodes were lost or unreadable and we selected a new plant closest to the original position (independent of age, length, or condition) and marked it with a new unique barcode. We measured the size of the vanilla agroforest by walking with the agroforest owner and a hand-held GPS device at the perimeter of the plot.Vanilla planting densityWe counted each vanilla pied on each 25 m circular plot by dividing the plot in four-quarter segments. We calculated the area of each 25 m radius plot including slope correction and calculated vanilla planting density (vanilla pieds per hectare) by dividing the number of vanilla pieds by the slope-corrected plot area.Vanilla yieldWe measured yield on 30 vanilla plantations (10 forest-derived vanilla plantations and 20 fallow-derived vanilla plantations); three in each of our 10 study villages. We measured vanilla yield on a total of 36 vanilla pieds between March and April 2018. We assessed the vanilla yield before harvest to ensure an accurate yield assessment due to two reasons. Firstly, vanilla pods are commonly harvested successively due to their differing pollination date and maturity requiring multiple visits over several weeks. Secondly, theft of vanilla pods is commonplace around harvest time. We, therefore, estimated the weight of the on-plant-hanging vanilla pods by measuring pod volume and relating this to a prior established volume–weight correlation. This is possible because vanilla pods only grow in length and width in the first 8 weeks of their development76. Our yield assessment consisted of one interview part with the plot owner and one measurement part. The interview part included questions about the occurrence of theft and early harvest on the plantation. During the measurement part, we assessed the number, diameter, and length of all vanilla pods. We measured vanilla pod length with a ruler starting at the junction of stem and pod until the tip of the pod without considering the bending of the pod. We measured the diameter at the widest part of the pod using a caliper. We firstly calculated pod volume based on the standard volume cylinder formula using the measured diameter (cm) and length (cm): V = πr2h.Secondly, we calculated the weight (g) of each pod by using the linear regression equation (y = bx + a) of a weight–volume correlation of 114 vanilla pods from 114 different agroforests (weight, length, and diameter of these 114 green vanilla was assessed post-harvest in 2017). We calculated the weight of all measured pods of the harvest in 2018 based on the formula:$${{{{{rm{volume}}}}}}={{{{{rm{pi }}}}}}({{{{{rm{diameter}}}}}}({{{{{rm{mm}}}}}})/20)^wedge 2ast {{{{{rm{length}}}}}}({{{{{rm{cm}}}}}})$$Here, we divided the pod diameter (mm) by 20 to obtain the radius and to transform millimeters to centimeters. Weight was defined as volume*0.5662 + 0.9699. No vanilla pods were stolen or already harvested on our 36 vanilla pieds and hence we did not need to account for it in our vanilla yield calculation.Vanilla vine lengthWe assessed vanilla vine length for all 36 vanilla pieds (same vanilla pieds as used for the yield assessment) on each plot by measuring the total length of the vine from the lowest to the highest part with a measuring stick. If the vanilla vine was looped on the support tree (= vanilla vine is hanging in multiple loops on the support tree), we measured from the top height of the looping of the vanilla vine until the lowest height of the vine. At the medium height of the vanilla vine, we counted the number of times the vanilla vine passed through. We calculated the total length of the liana by multiplying the maximum height of the vanilla vine by the number of times the vine passed through the middle. In some cases, the vanilla vine looped at two different heights, we thus considered the middle between the two looping heights as the top height. If vanilla vines grew on two different support trees, we considered them as one vanilla pieds if support trees were More

Hu ZM, Li SG, Guo Q, Niu SL, He NP, Li LH. et al. A synthesis of the effect of grazing exclusion on carbon dynamics in grasslands in China. Global Change Biol. 2016;22:1385–93.Article 

Google Scholar 
Lyu X, Li XB, Gong JR, Wang H, Dang DL, Dou HS, et al. Comprehensive grassland degradation monitoring by remote sensing in Xilinhot, Inner Mongolia, China. Sustainability. 2020;12:3682.Article 

Google Scholar 
O’Mara FP. The role of grasslands in food security and climate change. Ann Bot-London. 2012;110:1263–70.Article 

Google Scholar 
Bryan BA, Gao L, Ye YQ, Sun XF, Connor JD, Crossman ND, et al. China’s response to a national land-system sustainability emergency. Nature. 2018;559:193–204.CAS 
PubMed 
Article 

Google Scholar 
Bardgett RD, Bullock JM, Lavorel S, Manning P, Schaffner U, Ostle N. et al. Combatting global grassland degradation. Nat Rev Earth Environ. 2021;2:720–35.Article 

Google Scholar 
Chang JF, Ciais P, Gasser T, Smith P, Herrero M, Havlik P, et al. Climate warming from managed grasslands cancels the cooling effect of carbon sinks in sparsely grazed and natural grasslands. Nat Commun. 2021;12:118.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wardle DA, Bardgett RD, Klironomos JN, Setälä H, van der Putten WH, Wall DH. Ecological linkages between aboveground and belowground biota. Science. 2004;304:1629–33.CAS 
PubMed 
Article 

Google Scholar 
Feeney DS, Crawford JW, Daniell T, Hallett PD, Nunan N, Ritz K, et al. Three-dimensional microorganization of the soil-root-microbe system. Microb Ecol. 2006;52:151–8.PubMed 
Article 

Google Scholar 
Harris J. Soil microbial communities and restoration ecology: Facilitators or followers? Science. 2009;325:573–4.CAS 
PubMed 
Article 

Google Scholar 
Vecrin MP, Muller S. Top-soil translocation as a technique in the re-creation of species-rich meadows. Appl Veg Sci. 2003;6:271–8.Article 

Google Scholar 
Middleton EL, Bever JD. Inoculation with a native soil community advances succession in a grassland restoration. Restor Ecol. 2012;20:218–26.Article 

Google Scholar 
Wubs ERJ, van der Putten WH, Bosch M, Bezemer TM. Soil inoculation steers restoration of terrestrial ecosystems. Nat Plants. 2016;2:16107.PubMed 
Article 

Google Scholar 
Wubs ERJ, van Heusden T, Melchers PD, Bezemer TM. Soil inoculation steers plant-soil feedback, suppressing ruderal plant species. Front Ecol Evol. 2019;7:451.Article 

Google Scholar 
Bever JD. Feedback between plants and their soil communities in an old field community. Ecology. 1994;75:1965–77.Article 

Google Scholar 
Bennett JA, Maherali H, Reinhart KO, Lekberg Y, Hart MM, Klironomos J. Plant-soil feedbacks and mycorrhizal type influence temperate forest population dynamics. Science. 2017;355:181–4.CAS 
PubMed 
Article 

Google Scholar 
Contos P, Wood JL, Murphy NP, Gibb H. Rewilding with invertebrates and microbes to restore ecosystems: Present trends and future directions. Ecol Evol. 2021;11:7187–200.PubMed 
PubMed Central 
Article 

Google Scholar 
Emam T. Local soil, but not commercial AMF inoculum, increases native and non-native grass growth at a mine restoration site. Restor Ecol. 2016;24:35–44.Article 

Google Scholar 
Moradi J, Vicentini F, Simackova H, Pizl V, Tajovsky K, Stary J. An investigation into the long-term effect of soil transplant in bare spoil heaps on survival and migration of soil meso and macrofauna. Ecol Eng. 2018;110:158–64.Article 

Google Scholar 
Carbajo V, den Braber B, van der Putten WH, De Deyn GB. Enhancement of late successional plants on ex-arable land by soil inoculations. Plos One. 2011;6:e21943.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ma W, Liang XS, Wang ZW, Luo WT, Yu Q, Han XG. Resistance of steppe communities to extreme drought in northeast China. Plant Soil. 2022;473:181–194.IUSS Working Group WRB. World Reference Base for Soil Resources 2014, update 2015 International soil classification system for naming soils and creating legends for soil maps. World Soil Resources Reports No. 106. FAO, Rome, 2015.Jaunatre R, Buisson E, Dutoit T. Topsoil removal improves various restoration treatments of a Mediterranean steppe (La Crau, southeast France). Appl Veg Sci. 2014;17:236–45.Article 

Google Scholar 
Kuo S. Methods of soil analysis. Part 3: chemical methods. Soil Science Society of America: Madison, 1996.Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. P Natl Acad Sci USA. 2008;105:10583–8.CAS 
Article 

Google Scholar 
De Beeck MO, Lievens B, Busschaert P, Declerck S, Vangronsveld J, Colpaert JV. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. Plos One. 2014;9:e97629.Article 

Google Scholar 
Magoč T, Salzberg SL. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.CAS 
PubMed 
Article 

Google Scholar 
Chen SF, Zhou YQ, Chen YR, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Edgar RC. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.CAS 
PubMed 
Article 

Google Scholar 
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb. 2007;73:5261–7.CAS 
Article 

Google Scholar 
Quast C, Pruesse E, Gerken J, Peplies J, Yarza P, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:590–6.Article 
CAS 

Google Scholar 
Kõljalg U, Larsson K-H, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005;166:1063–8.PubMed 
Article 
CAS 

Google Scholar 
Oostenbrink M. Estimating nematode populations by some selected methods. Nematology, Chapel Hill, 1960.Townshend JL. A modification and evaluation of the apparatus for the Oostenbrink direct cotton wool filter extraction method. Nematologica. 1963;9:106–10.Article 

Google Scholar 
Bongers T. De Nematoden van Nederland. In: Vormgeving en technische realisatie. Uitgeverij Pirola, Schoorl, 1994.Ahmad W, Jairjpuri MS. Mononchida: the predaceous nematodes. Nematology Monographs and Perspectives. Brill, Boston, 2010.Li Q, Liang WJ, Zhang XK, Mahamood M. Soil nematodes of grasslands in Northern China. Academic Press: San Diego, 2017.Wu ZY, Raven PH, Hong DY. Flora of China. Science Press: Beijing, 2013.Munson SM, Long AL, Wallace CSA, Webb RH. Cumulative drought and land-use impacts on perennial vegetation across a North American dryland region. Appl Veg Sci. 2016;19:430–41.Article 

Google Scholar 
Li YH, Wang W, Liu ZL, Jiang S. Grazing gradient versus restoration succession of leymus chinensis (Trin.) Tzvel. grassland in inner mongolia. Restor Ecol. 2008;16:572–83.Article 

Google Scholar 
Liang C, Michalk DL, Millar GD. The ecology and growth patterns of Cleistogenes species in degraded grasslands of eastern Inner Mongolia, China. J Appl Ecol. 2002;39:584–94.Article 

Google Scholar 
Liu ZG, Li ZQ. Effects of different grazing regimes on the morphological traits of Carex duriuscula on the Inner Mongolia steppe. China. New Zeal J Agr Res. 2010;53:5–12.Article 

Google Scholar 
Liu M, Gong JR, Pan Y, Luo QP, Zhai ZW, Yang LL, et al. Response of dominant grassland species in the temperate steppe of Inner Mongolia to different land uses at leaf and ecosystem levels. Photosynthetica. 2018;56:921–31.Article 

Google Scholar 
Bates D, Machler M, Bolker BM, Walker SC. Fitting linear mixed-effects models using lme4. J Stat Softw. 2015;67:1–48.Article 
CAS 

Google Scholar 
Dixon P. Vegan, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.Article 

Google Scholar 
McMurdie PJ, Holmes S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. Plos One. 2013;8:e61217.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.CAS 
PubMed 
Article 

Google Scholar 
De Cáceres M, Legendre P, Moretti M. Improving indicator species analysis by combining groups of sites. Oikos. 2010;119:1674–84.Article 

Google Scholar 
Hartman K, van der Heijden MGA, Wittwer RA, Banerjee S, Walser JC, Schlaeppi K. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome. 2018;6:14.PubMed 
PubMed Central 
Article 

Google Scholar 
Aitchison J. A new approach to null correlations of proportions. Mathematical Geology. 1981;13:175–89.Article 

Google Scholar 
Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. Plos Comput Biol. 2015;11:e1004226.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Cao YP, Lin W, Li HZ. Two-sample tests of high-dimensional means for compositional data. Biometrika. 2018;105:115–32.Article 

Google Scholar 
Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst. 2006;1695:1–9.Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16:567–76.CAS 
PubMed 
Article 

Google Scholar 
Banerjee S, Schlaeppi K, van der Heijden MGA. Reply to ‘Can we predict microbial keystones?’. Nat Rev Microbiol. 2019;17:194–194.CAS 
PubMed 
Article 

Google Scholar 
Zheng HP, Yang TJ, Bao YZ, He PP, Yang KM, Mei XL, et al. Network analysis and subsequent culturing reveal keystone taxa involved in microbial litter decomposition dynamics. Soil Biol Biochem. 2021;157:108230.CAS 
Article 

Google Scholar 
Kardol P, Wardle DA. How understanding aboveground-belowground linkages can assist restoration ecology. Trends Ecol Evol. 2010;25:670–9.PubMed 
Article 

Google Scholar 
Wubs ERJ, van der Putten WH, Mortimer SR, Korthals GW, Duyts H, Wagenaar R, et al. Single introductions of soil biota and plants generate long-term legacies in soil and plant community assembly. Ecol Lett. 2019;22:1145–51.PubMed 
PubMed Central 
Article 

Google Scholar 
St-Denis A, Kneeshaw D, Belanger N, Simard S, Laforest-Lapointe I, Messier C. Species-specific responses to forest soil inoculum in planted trees in an abandoned agricultural field. Appl Soil Ecol. 2017;112:1–10.Article 

Google Scholar 
Kitto JAJ, Gray DP, Greig HS, Niyogi DK, Harding JS. Meta-community theory and stream restoration: evidence that spatial position constrains stream invertebrate communities in a mine impacted landscape. Restor Ecol. 2015;23:284–91.Article 

Google Scholar 
Ofek M, Hadar Y, Minz D. Ecology of root colonizing Massilia (Oxalobacteraceae). Plos One. 2012;7:e40117.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lyu D, Backer R, Smith DL. Three plant growth-promoting rhizobacteria alter morphological development, physiology, and flower yield of Cannabis sativa L. Ind Crop Prod. 2022;178:114583.CAS 
Article 

Google Scholar 
Kulmatiski A, Beard KH. Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure. Soil Biol Biochem. 2011;43:823–30.CAS 
Article 

Google Scholar 
Brewer TE, Handley KM, Carini P, Gilbert JA, Fierer N. Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’. Nat Microbiol. 2017;2:16198.Article 
CAS 

Google Scholar 
Reme J. Development and present state of close-to-nature silviculture. J Landscape Ecol. 2018;11:17–32.Article 

Google Scholar  More

Nathan, R. et al. A movement ecology paradigm for unifying organismal movement research. Proc. Natl. Acad. Sci. 105, 19052–19059 (2008).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lima, S. L. & Dill, L. M. Behavioral decisions made under the risk of predation: A review and prospectus. Can. J. Zool. 68, 619–640 (1990).Article 

Google Scholar 
Kays, R., Crofoot, M. C., Jetz, W. & Wikelski, M. Terrestrial animal tracking as an eye on life and planet. Science 348, 1122–1133. https://doi.org/10.1126/science.aaa2478 (2015).CAS 
Article 

Google Scholar 
Allen, A. M. & Singh, N. J. Linking movement ecology with wildlife management and conservation. Front. Ecol. Evol. 3, 1–13. https://doi.org/10.3389/fevo.2015.00155 (2016).ADS 
Article 

Google Scholar 
Fraser, K. C. et al. Tracking the conservation promise of movement ecology. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2018.00150 (2018).Article 

Google Scholar 
Boutin, S. Food supplementation experiments with terrestrial vertebrates: Patterns, problems, and the future. Can. J. Zool. 68, 203–220 (1990).Article 

Google Scholar 
Adams, E. S. Approaches to the study of territory size and shape. Annu. Rev. Ecol. Syst. 32, 277–303. https://doi.org/10.1146/annurev.ecolsys.32.081501.114034 (2001).Article 

Google Scholar 
Ruffino, L., Salo, P., Koivisto, E., Banks, P. B. & Korpimaki, E. Reproductive responses of birds to experimental food supplementation: A meta-analysis. Front. Ecol. Evol. 11, 1–13. https://doi.org/10.1186/s12983-014-0080-y (2014).CAS 
Article 

Google Scholar 
Taylor, E. N., Malawy, M. A., Browning, D. M., Lemar, S. V. & DeNardo, D. F. Effects of food supplementation on the physiological ecology of female western diamond-backed rattlesnakes (Crotalus atrox). Oecologia 144, 206–213. https://doi.org/10.1007/s00442-005-0056-x (2005).ADS 
Article 
PubMed 

Google Scholar 
Wasko, D. K. & Sasa, M. Food resources influence spatial ecology, habitat selection, and foraging behavior in an ambush-hunting snake (Viperidae: Bothrops asper): An experimental study. Zoology 115, 179–187. https://doi.org/10.1016/j.zool.2011.10.001 (2012).Article 
PubMed 

Google Scholar 
Glaudas, X. & Alexander, G. J. Food supplementation affects the foraging ecology of a low-energy, ambush-foraging snake. Behav. Ecol. Sociobiol. 71, 1–11. https://doi.org/10.1007/s00265-016-2239-3 (2017).Article 

Google Scholar 
Secor, S. M. & Nagy, K. A. Bioenergetic correlates of foraging mode for the snakes Crotalus cerastes and Masticophis flagellum. Ecology 75, 1600–1614 (1994).Article 

Google Scholar 
Christy, M. T., Savidge, J. A., Yackel Adams, A. A., Gragg, J. E. & Rodda, G. H. Experimental landscape reduction of wild rodents increases movements in the invasive brown treesnake (Boiga irregularis). Manag. Biol. Invasions 8, 455–467. https://doi.org/10.3391/mbi.2017.8.4.01 (2017).Article 

Google Scholar 
Neilson, E. W., Avgar, T., Burton, A. C., Broadley, K. & Boutin, S. Animal movement affects interpretation of occupancy models from camera-trap surveys of unmarked animals. Ecosphere 9, 1–15. https://doi.org/10.1002/ecs2.2092 (2018).Article 

Google Scholar 
Efford, M. G. & Dawson, D. K. Occupancy in continuous habitat. Ecosphere 3, 1–15. https://doi.org/10.1890/ES11-00308.1 (2012).Article 

Google Scholar 
Tang, Z., Huang, Q., Wu, H., Kuang, L. & Fu, S. The behavioral response of prey fish to predators: The role of predator size. PeerJ 5, 1–13. https://doi.org/10.7717/peerj.3222 (2017).Article 

Google Scholar 
Thorsen, M., Shorten, R., Lucking, R. & Lucking, V. Norway rats (Rattus norvegicus) on Fregate Island, Seychelles: The invasion; subsequent eradication attempts and implications for the island’s fauna. Biol. Cons. 96, 133–138 (2000).Article 

Google Scholar 
Rodda, G. H. Foraging behavior of the brown tree snake, Boiga irregularis. Herpetol. J. 2, 110–114 (1992).
Google Scholar 
Savidge, J. A. Extinction of an island forest avifauna by an introduced snake. Ecology 68, 660–668 (1987).Article 

Google Scholar 
Rodda, G. H., McCoid, M. J., Fritts, T. H. & Campbell, E. W. III. Population trends and limiting factors in Boiga irregularis. In Problem Snake Management: The Habu and the Brown Treesnake (eds Rodda, G. H. et al.) 236–256 (Cornell University Press, 1999).Chapter 

Google Scholar 
Yackel Adams, A. A., Lardner, B., Knox, A. J. & Reed, R. N. Inferring the absence of an incipient population during a rapid response for an invasive species. PLoS ONE 13, 1–13 (2018).Article 
CAS 

Google Scholar 
Clark, L., Clark, C. & Siers, S. Brown tree snake methods and approaches for control. In Ecology and Management of Terrestrial Vertebrate Invasive Species in the United States (eds Pitt, W. C. et al.) 107–134 (CRC Press, 2018).
Google Scholar 
Christy, M. T., Yackel Adams, A. A., Rodda, G. H., Savidge, J. A. & Tyrrell, C. L. Modelling detection probabilities to evaluate management and control tools for an invasive species. J. Appl. Ecol. 47, 106–113 (2010).Article 

Google Scholar 
Tyrrell, C. L. et al. Evaluation of trap capture in a geographically closed population of brown treesnakes on Guam. J. Appl. Ecol. 46, 128–135 (2009).Article 

Google Scholar 
Siers, S. R., Yackel Adams, A. A. & Reed, R. N. Behavioral differences following ingestion of large meals and consequences for management of a harmful invasive snake: A field experiment. Ecol. Evol. 8, 10075–10093 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Santana-Bendix, M. A. Movements, Activity Patterns and Habitat Use of Boiga irregularis (Colubridae), an Introduced Predator in the Island of Guam (University of Arizona, 1994).
Google Scholar 
Tobin, M. E., Sugihara, R. T., Pochop, P. A. & Linnell, M. A. Nightly and seasonal movements of Boiga irregularis on Guam. J. Herpetol. 33, 281–291 (1999).Article 

Google Scholar 
Lardner, B., Savidge, J. A., Reed, R. N. & Rodda, G. H. Movements and activity of juvenile brown treesnakes (Boiga irregularis). Copeia 2014, 428–436 (2014).Article 

Google Scholar 
Siers, S. R., Savidge, J. A. & Reed, R. N. Invasive brown treesnake movements at road edges indicate road-crossing avoidance. J. Herpetol. 48, 500–505 (2014).Article 

Google Scholar 
Wiewel, A. S., Yackel Adams, A. A. & Rodda, G. H. Distribution, density, and biomass of introduced small mammals in the southern Marian Islands. Pac. Sci. 63, 205–222 (2009).Article 

Google Scholar 
Camp, R. J., Amidon, F. A., Marshall, A. P. & Pratt, T. K. Bird populations on the island of Tinian; Persistence despite wholesale loss of native forests. Pac. Sci. 66, 283–298. https://doi.org/10.2984/66.3.3 (2012).Article 

Google Scholar 
Lardner, B., Yackel Adams, A. A., Knox, A. J., Savidge, J. A. & Reed, R. N. Do observer fatigue and taxon bias compromise visual encounter surveys for small vertebrates?. Wildl. Res. 46, 127–135 (2019).Article 

Google Scholar 
Mathies, T., Levine, B., Engeman, R. & Savidge, J. A. Pheromonal control of the invasive brown treesnake: Potency of female sexual attractiveness pheromone varies with ovarian state. Int. J. Pest Manag. https://doi.org/10.1080/09670874.2013.784374 (2013).Article 

Google Scholar 
Boback, S. M., Nafus, M. G., Yackel Adams, A. A. & Reed, R. N. Use of visual surveys and radiotelemetry reveals sources of detection bias for a cryptic snake at low densities. Ecosphere https://doi.org/10.1002/ecs2.3000 (2020).Article 

Google Scholar 
Harper, G. A. & Rutherford, M. Home range and population density of black rats (Rattus rattus) on a seabird island: A case for a marine subsidised effect?. N. Z. J. Ecol. 40, 219–228 (2016).
Google Scholar 
Hochachka, W. M., Martin, K., Doyle, F. & Krebs, C. J. Monitoring vertebrate populations using observational data. Can. J. Zool. 78, 521–529 (2000).Article 

Google Scholar 
Wiewel, A. S., Yackel Adams, A. A. & Rodda, G. H. Evaluating abundance estimate precision and the assumptions of a count-based index for small mammals. J. Wildl. Manag. 73, 761–771. https://doi.org/10.2193/2008-180 (2009).Article 

Google Scholar 
Fauteux, D. et al. Evaluation of invasive and non-invasive methods to monitor rodent abundance in the Arctic. Ecosphere 9, 1–18. https://doi.org/10.1002/ecs2.2124 (2018).Article 

Google Scholar 
Siers, S. R. et al. Assessment of brown treesnake activity and bait take following large-scale snake suppression in Guam. (ed APHIS USDA, WS, NWRC) (Final Report QA-2438, Hilo, HI, 2018).McQueen, D. J., Post, J. R. & Mills, E. L. Trophic relationships in fresh-water pelagic ecosystems. Can. J. Fish. Aquat. Sci. 43, 1571–1581 (1986).Article 

Google Scholar 
Sih, A., Crowley, P., McPeek, M., Petranka, J. & Strohmeier, K. Predation, competition, and prey communities: A review of field experiments. Annu. Rev. Ecol. Syst. 16, 269–311 (1985).Article 

Google Scholar 
Dorcas, M. E. et al. Severe mammal declines coincide with proliferation of invasive Burmese pythons in Everglades National Park. Proc. Natl. Acad. Sci. 109, 2418–2422. https://doi.org/10.1073/pnas.1115226109 (2012).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
de Miranda, E. B. P. The plight of reptiles as ecological actors in the tropics. Front. Ecol. Evol. 5, 1–15. https://doi.org/10.3389/fevo.2017.00159 (2017).Article 

Google Scholar 
Campbell, E. W. III., Yackel Adams, A. A., Converse, S. J., Fritts, T. H. & Rodda, G. H. Do predators control prey species abundance? An experimental test with brown treesnakes on Guam. Ecology 93, 1194–1203 (2012).PubMed 
Article 

Google Scholar 
Lindell, L. E. & Forsman, A. Density effects and snake predation: Prey limitation and reduced growth rate of adders at high density of conspecifics. Can. J. Zool. 74, 1000–1007 (1996).Article 

Google Scholar 
Schoener, T. W., Spiller, D. A. & Losos, J. B. Predation on a common Anolis lizard: Can the food-web effects of a devastating predator be reversed?. Ecol. Monogr. 72, 383–407 (2002).Article 

Google Scholar 
McCleery, R. A. et al. Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades. Proc. R. Soc. Lond. 282, 20150120. https://doi.org/10.1098/rspb.2015.0120 (2015).Article 

Google Scholar 
Plummer, M. V. & Congdon, J. D. Radiotelemetric study of activity and movements of racers (Coluber constrictor) associated with a Carolina bay in South Carolina. Copeia 1994, 20–26 (1994).Article 

Google Scholar 
Madsen, T. & Shine, R. Seasonal migration of predators and prey—A study of pythons, and rats in tropical Australia. Ecology 77, 149–156 (1996).Article 

Google Scholar 
Chandler, C. J., Van Helden, B., Close, P. G. & Speldewinde, P. C. 2D or not 2D? Three-dimensional home range analysis better represents space use by an arboreal mammal. Acta Oecol. 105, 103576. https://doi.org/10.1016/j.actao.2020.103576 (2020).Article 

Google Scholar 
Udyawer, V., Simpfendorfer, C. A. & Heupel, M. R. Diel patterns in three-dimensional use of space by sea snakes. Anim. Biotelem. 3, 1–9. https://doi.org/10.1186/s40317-015-0063-6 (2015).Article 

Google Scholar 
Shine, R. Reproduction in Australian elapid snakes II. Female reproductive cycles. Aust. J. Zool. 25, 655–666 (1977).Article 

Google Scholar 
Murcia, C. Edge effects in fragmented forests: Implications for conservation. Trends Ecol. Evol. 10, 58–62 (1995).CAS 
PubMed 
Article 

Google Scholar 
Matlack, G. R. Microenvironment variation within and among forest edge sites in the eastern United States. Biol. Cons. 66, 185–194 (1993).Article 

Google Scholar 
Kapos, V. Effects of isolation on the water status of forest patches in the Brazilian Amazon. Trop. Ecol. 5, 173–185 (1989).Article 

Google Scholar 
Williams-Linera, G. Vegetation structure and environmental conditions of forest edges in Panama. J. Ecol. 78, 356–373 (1990).Article 

Google Scholar 
Matlack, G. R. Vegetation dynamics of the forest edge: Trends in space and successional time. J. Ecol. 82, 113–123 (1994).Article 

Google Scholar 
Chen, J., Franklin, J. F. & Spies, T. A. Vegetation responses to edge environments in old-growth douglas-fir forests. Ecol. Appl. 2, 387–396 (1992).PubMed 
Article 

Google Scholar 
Gates, J. E. Powerline corridors, edge effects, and wildlife in forested landscapes of the central Appalachians. In Wildlife and Habitats in Managed Landscapes (eds Rodiek, J. E. & Bolen, E. G.) 13–32 (Island Press, 1991).
Google Scholar 
Kroodsma, R. L. Edge effect on breeding forest birds along a power-line corridor. J. Appl. Ecol. 19, 361–370 (1982).Article 

Google Scholar 
Morgan, K. A. & Gates, J. E. Bird population patterns in forest edge and strip vegetation at Remington Farms, Maryland. J. Wildl. Manag. 46, 933–944 (1982).Article 

Google Scholar 
Weatherhead, P. J. & Charland, M. B. Habitat selection in an Ontario population of the snake, Elaphe obsoleta. J. Herpetol. 19, 12–19 (1985).Article 

Google Scholar 
Durner, G. M. & Gates, J. E. Spatial ecology of black rat snakes on Remington Farms, Maryland. J. Wildl. Manag. 57, 812–826 (1993).Article 

Google Scholar 
Mushinsky, H. R. Foraging ecology. In Snakes: Ecology and Evolutionary Biology (eds Seigel, R. A. et al.) 302–334 (Macmillan Publishing Company, 1987).
Google Scholar 
Fritts, T. H., Scott, N. J. Jr. & Smith, B. J. Trapping Boiga irregularis on Guam using bird odors. J. Herpetol. 23, 189–192 (1989).Article 

Google Scholar 
Shivik, J. A. Brown tree snake response to visual and olfactory cues. J. Wildl. Manag. 62, 105–111 (1998).Article 

Google Scholar 
Simkova, O., Frydlova, P., Zampachova, B., Frynta, D. & Landova, E. Development of behavioral profile in the Northern common boa (Boa imperator): Repeatable independent traits or personality?. PLoS ONE 12, 1–35. https://doi.org/10.1371/journal.pone.0177911 (2017).CAS 
Article 

Google Scholar 
Fritts, T. H., McCoid, M. J. & Gomez, D. M. Dispersal of snakes to extralimital islands: Incidents of the brown treesnake, Boiga irregularis, dispersing to islands in ships and aircraft. In Problem Snake Management: The Habu and the Brown Treesnake (eds Rodda, G. H. et al.) 209–223 (Cornell University Press, 1999).
Google Scholar 
Yackel Adams, A. A. et al. Can we prove that an undetected species is absent? Evaluating whether brown treesnakes are established on the island of Saipan using surveillance and expert opinion. Manag. Biol. Invas. 12, 901–926 (2021).Article 

Google Scholar 
Siers, S. R. & Savidge, J. A. Restoration Plan for the Habitat Management Unit, Naval Support Activity Andersen, Guam 1–238 (Colorado State University, 2017).
Google Scholar 
Dorr, B. S., Clark, C. S. & Savarie, P. (USDA APHIS WS National Wildlife Research Center, Fort Collins, CO, 2016).Reinert, H. K. & Cundall, D. An improved surgical implantation method for radio-tracking snakes. Copeia 1982, 702–705 (1982).Article 

Google Scholar 
Shine, R. Strangers in a strange land: Ecology of the Australian colubrid snakes. Copeia 1991, 120–131 (1991).Article 

Google Scholar 
Savidge, J. A., Qualls, F. J. & Rodda, G. H. Reproductive biology of the brown tree snake, Boiga irregularis (Reptilia: Colubridae), during colonization of Guam and comparison with that in their native range. Pac. Sci. 61, 191–199 (2007).Article 

Google Scholar 
Yackel Adams, A. A. & Nafus, M. G. Brown Treesnake visual survey and radiotelemetry data, Guam 2015: U.S. Geological Survey data release. https://doi.org/10.5066/P939BM0W (2020).Savidge, J. A. Food habits of Boiga irregularis, an introduced predator on Guam. J. Herpetol. 22, 275–282 (1988).Article 

Google Scholar 
Reed, R. N. & Boback, S. M. Does body size predict dates of species description among North American and Australian reptiles and amphibians?. Glob. Ecol. Biogeogr. 11, 41–47 (2002).Article 

Google Scholar 
Duong, T. ks: Kernel density estimation and kernel discriminant analysis for multivariate data in R. J. Stat. Softw. 21, 1–16 (2007).Article 

Google Scholar 
R Foundation for Statistical Computing. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2017).
Google Scholar 
Simpfendorfer, C. A., Olsen, E. M., Heupel, M. R. & Moland, E. Three-dimensional kernel utilization distributions improve estimates of space use in aquatic animals. Can. J. Fish. Aquat. Sci. 69, 565–572 (2012).Article 

Google Scholar 
Gitzen, R. A., Millspaugh, J. J. & Kernohan, B. J. Bandwidth selection for fixed-kernel analysis of animal utilization distributions. J. Wildl. Manag. 70, 1334–1344 (2006).Article 

Google Scholar 
Cooper, N. W., Sherry, T. W. & Marra, P. P. Modeling three-dimensional space use and overlap in birds. Auk 131, 681–693 (2014).Article 

Google Scholar 
ArcGIS Desktop (Environmental Systems Research, 2017).Nafus, M. G., Boback, S. M., Klug, P. E., Yackel Adams, A. A. & Reed, R. N. Brown treesnake movement following snake suppression in the Habitat Management Unit on Northern Guam from 2015. U.S Geological Survey data release. https://doi.org/10.5066/P95QJ2PE (2022). More

Ramoliya, P. & Pandey, A. Effect of salinization of soil on emergence, growth and survival of seedlings of Cordia rothii. For. Ecol. Manage. 176, 185–194 (2003).Article 

Google Scholar 
Müller, H. M. et al. The desert plant Phoenix dactylifera closes stomata via nitrate-regulated SLAC1 anion channel. New Phytol. 216, 150–162 (2017).PubMed 
Article 
CAS 

Google Scholar 
Hazzouri, K. M. et al. Prospects for the study and improvement of abiotic stress tolerance in date palms in the post-genomics era. Front. Plant Sci. 11, 293 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Abdelfattah, M. A. Integrated suitability assessment: A way forward for land use planning and sustainable development in Abu Dhabi, United Arab Emirates. Arid Land Res. Manage. 27, 41–64 (2013).Article 

Google Scholar 
Al-Muaini, A. et al. Water requirements for irrigation with saline groundwater of three date-palm cultivars with different salt-tolerances in the hyper-arid United Arab Emirates. Agric. Water Manage. 222, 213–220 (2019).Article 

Google Scholar 
Guo, H., Shi, X., Ma, L., Yang, T. & Min, W. Long-term irrigation with saline water decreases soil nutrients, diversity of bacterial communities, and cotton yields in a gray desert soil in China. Pol. J. Environ. Stud. 29, 4077–4088 (2020).CAS 
Article 

Google Scholar 
Blaskó, L. Salinity, physical effects on soils. In Encyclopedia of Agrophysics (eds Gliński, J. et al.) 723–725 (Springer, 2011).Chapter 

Google Scholar 
Rengasamy, P. Irrigation water quality and soil structural stability: A perspective with some new insights. Agronomy 8, 72 (2018).Article 
CAS 

Google Scholar 
Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: From community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).CAS 
PubMed 
Article 

Google Scholar 
Masmoudi, K. et al. Metagenomics of beneficial microbes in abiotic stress tolerance of date palm. In The Date Palm Genome, Vol. 2: Omics and Molecular Breeding (eds Al-Khayri, J. M. et al.) 203–214 (Springer, 2021).Chapter 

Google Scholar 
Boncompagni, E., Østerås, M., Poggi, M.-C. & Le Rudulier, D. Occurrence of choline and glycine betaine uptake and metabolism in the family rhizobiaceae and their roles in osmoprotection. Appl. Environ. Microbiol. 65, 2072–2077 (1999).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chen, C. & Beattie, G. A. Characterization of the osmoprotectant transporter opuc from Pseudomonas syringae and demonstration that cystathionine-β-synthase domains are required for its osmoregulatory function. J. Bacteriol. 189, 6901–6912 (2007).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rath, H. et al. Management of osmoprotectant uptake hierarchy in Bacillus subtilis via a SigB-dependent antisense RNA. Front. Microbiol. 11, 622 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Singh, R. P. & Jha, P. N. The PGPR Stenotrophomonas maltophilia SBP-9 augments resistance against biotic and abiotic stress in wheat plants. Front. Microbiol. 8, 1945 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Ferjani, R. et al. The date palm tree rhizosphere is a niche for plant growth promoting bacteria in the oasis ecosystem. Biomed Res. Int. 2015, 1–10 (2015).Article 

Google Scholar 
Sanka Loganathachetti, D., Alhashmi, F., Chandran, S. & Mundra, S. Irrigation water salinity structures the bacterial communities of date palm (Phoenix dactylifera)-associated bulk soil. Front. Plant Sci. https://doi.org/10.3389/fpls.2022.944637 (2022).Article 

Google Scholar 
Chen, L. J. et al. An integrative influence of saline water irrigation and fertilization on the structure of soil bacterial communities. J. Agric. Sci. 157, 693–700 (2019).CAS 
Article 

Google Scholar 
Li, Y. Q. et al. Bacterial community in saline farmland soil on the Tibetan plateau: Responding to salinization while resisting extreme environments. BMC Microbiol. 21, 119 (2021).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Mosqueira, M. J. et al. Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems. Sci. Rep. 9, 4033 (2019).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Cherif, H. et al. Oasis desert farming selects environment-specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought. Environ. Microbiol. Rep. 7, 668–678 (2015).CAS 
PubMed 
Article 

Google Scholar 
FAO. Standard Operating Procedure for Soil Electrical Conductivity, Soil/Water, 1:5. (2021).Nelson, D. W. & Sommers, L. E. Total carbon, organic carbon, and organic matter. In Chemical Methods-SSSA Book Series No. 5 (eds Bigham, J. M. et al.) (Soil Science Society of America and American Society of Agronomy, 1996).
Google Scholar 
Mizrahi-Man, O., Davenport, E. R. & Gilad, Y. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: Evaluation of effective study designs. PLoS ONE 8, e53608 (2013).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Martin-Sanchez, P. M. et al. Analysing indoor mycobiomes through a large-scale citizen science study in Norway. Mol. Ecol. 30, 2689–2705 (2021).CAS 
PubMed 
Article 

Google Scholar 
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Dai, T. et al. Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: A case study of microbial communities in the sediments of Hangzhou Bay. FEMS Microbiol. Ecol. 92, 150 (2016).Article 
CAS 

Google Scholar 
Oksanen, J. et al. vegan: Community Ecology Package (2020).Blanchet, F. G., Legendre, P. & Borcard, D. Forward selection of explanatory variables. Ecology 89, 2623–2632 (2008).PubMed 
Article 

Google Scholar 
Emirates Soil Museum. Emirates Soil Museum. https://www.emiratessoilmuseum.org/index.php/ (Accessed 08 July 2022).Jackson, O., Quilliam, R. S., Stott, A., Grant, H. & Subke, J.-A. Rhizosphere carbon supply accelerates soil organic matter decomposition in the presence of fresh organic substrates. Plant Soil 440, 473–490 (2019).CAS 
Article 

Google Scholar 
Xie, E. et al. Short-term effects of salt stress on the amino acids of Phragmites australis root exudates in constructed wetlands. Water 12, 569 (2020).CAS 
Article 

Google Scholar 
Korber, D. R., Choi, A., Wolfaardt, G. M. & Caldwell, D. E. Bacterial plasmolysis as a physical indicator of viability. Appl. Environ. Microbiol. 62, 3939–3947 (1996).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhang, K. et al. Salinity is a key determinant for soil microbial communities in a desert ecosystem. mSystems 4, e00225 (2019).CAS 
PubMed 
PubMed Central 

Google Scholar 
Hessini, K. et al. Interactive effects of salinity and nitrogen forms on plant growth, photosynthesis and osmotic adjustment in maize. Plant Physiol. Biochem. 139, 171–178 (2019).CAS 
PubMed 
Article 

Google Scholar 
Lammel, D. R. et al. Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures. Microbiome 6, 106 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Lopes, L. D., Hao, J. & Schachtman, D. P. Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem. FEMS Microbiol. Ecol. 97, 028 (2021).Article 
CAS 

Google Scholar 
Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351 (2010).PubMed 
Article 

Google Scholar 
Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Kumar, A., Mann, A., Kumar, A., Kumar, N. & Meena, B. L. Physiological response of diverse halophytes to high salinity through ionic accumulation and ROS scavenging. Int. J. Phytoremediat. 23, 1041–1051 (2021).CAS 
Article 

Google Scholar 
Kalam, S. et al. Recent understanding of soil acidobacteria and their ecological significance: A critical review. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.580024 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Boukhatem, Z. F., Merabet, C. & Tsaki, H. Plant growth promoting actinobacteria, the most promising candidates as bioinoculants? Front. Agron. https://doi.org/10.3389/fagro.2022.849911 (2022).Article 

Google Scholar 
Köberl, M. et al. Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity. FEMS Microbiol. Ecol. 92, 166 (2016).Article 
CAS 

Google Scholar 
Speirs, L. B. M., Rice, D. T. F., Petrovski, S. & Seviour, R. J. The phylogeny, biodiversity, and ecology of the Chloroflexi in activated sludge. Front. Microbiol. 10, 2015 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Hou, Y. et al. Responses of the soil microbial community to salinity stress in maize fields. Biology (Basel) 10, 1114 (2021).CAS 

Google Scholar 
Patil, A., Kale, A., Ajane, G., Sheikh, R. & Patil, S. Plant growth-promoting rhizobium: Mechanisms and biotechnological prospective. Rhizobium Biol. Biotechnol. https://doi.org/10.1007/978-3-319-64982-5_7 (2017).Article 

Google Scholar 
Lima Guimarães, S. et al. Effects of inoculation of Rhizobium on nodulation and nitrogen accumulation in cowpea subjected to water availabilities. Am. J. Plant Sci. 06, 1378–1384 (2015).Article 

Google Scholar 
Ghadbane, M., Medjekal, S., Benderradji, L., Belhadj, H. & Daoud, H. Assessment of arbuscular mycorrhizal fungi status and Rhizobium on date palm (Phoenix dactylifera L.) cultivated in a Pb contaminated soil. In Recent Advances in Environmental Science from the Euro-Mediterranean and Surrounding Regions 2nd edn (eds Ksibi, M. et al.) 703–707 (Springer, 2021).
Google Scholar 
Saeed, E. E. et al. Streptomyces globosus UAE1, a potential effective biocontrol agent for black scorch disease in date palm plantations. Front. Microbiol. 8, 1455 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Falagán, C. & Johnson, D. B. Acidibacter ferrireducens gen. nov., sp. nov.: An acidophilic ferric iron-reducing gammaproteobacterium. Extremophiles 18, 1067–1073 (2014).PubMed 
Article 
CAS 

Google Scholar 
Schulze-Makuch, D. et al. Transitory microbial habitat in the hyperarid Atacama desert. Proc. Natl. Acad. Sci. 115, 2670–2675 (2018).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhao, K. et al. Actinobacteria associated with Glycyrrhiza inflata Bat. are diverse and have plant growth promoting and antimicrobial activity. Sci. Rep. 8, 13661 (2018).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
An, S.-U. et al. Invasive Spartina anglica greatly alters the rates and pathways of organic carbon oxidation and associated microbial communities in an intertidal wetland of the Han river estuary, Yellow Sea. Front. Mar. Sci. 7, 59 (2020).ADS 
Article 

Google Scholar 
Khan, M. A. et al. Rhizospheric Bacillus spp. rescues plant growth under salinity stress via regulating gene expression, endogenous hormones, and antioxidant system of Oryza sativa L.. Front. Plant Sci. 12, 1145 (2021).
Google Scholar 
Schimel, J., Balser, T. C. & Wallenstein, M. Microbial stress-response physiology and its implications for ecosystem function. Ecology 88, 1386–1394 (2007).PubMed 
Article 

Google Scholar 
Mukhtar, S., Mehnaz, S., Mirza, M. S., Mirza, B. S. & Malik, K. A. Diversity of bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola), and characterization of osmoregulatory genes in halophilic Bacilli. Can. J. Microbiol. 64, 567–579 (2018).CAS 
PubMed 
Article 

Google Scholar 
Yeager, C. M. et al. Polysaccharide degradation capability of actinomycetales soil isolates from a semiarid grassland of the colorado plateau. Appl. Environ. Microbiol. 83, e03020-e3116 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ortúzar, M., Trujillo, M. E., Román-Ponce, B. & Carro, L. Micromonospora metallophores: A plant growth promotion trait useful for bacterial-assisted phytoremediation? Sci. Total Environ. 739, 139850 (2020).ADS 
PubMed 
Article 
CAS 

Google Scholar 
El-Tarabily, K. A. et al. Growth promotion of Salicornia bigelovii by Micromonospora chalcea UAE1, an endophytic 1-aminocyclopropane-1-carboxylic acid deaminase-producing actinobacterial isolate. Front. Microbiol. 10, 1694 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Carro, L. et al. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci. Rep. 8, 525 (2018).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Li, M. et al. Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields. Chin. Med. 15, 85 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rufián, J. S., Rueda-Blanco, J., Beuzón, C. R. & Ruiz-Albert, J. Protocol: An improved method to quantify activation of systemic acquired resistance (SAR). Plant Methods 15, 16 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Bhise, K. K., Bhagwat, P. K. & Dandge, P. B. Synergistic effect of Chryseobacterium gleum sp. SUK with ACC deaminase activity in alleviation of salt stress and plant growth promotion in Triticum aestivum L.. 3 Biotech 7, 105 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Cao, C., Tao, S., Cui, Z. & Zhang, Y. Response of soil properties and microbial communities to increasing salinization in the meadow grassland of Northeast China. Microb. Ecol. 82, 722–735 (2021).CAS 
PubMed 
Article 

Google Scholar  More