Philippa Kaur

Study area and soil collectionTwenty NRCS map units were selected across Hawaii Commercial & Sugar Company (HC&S) in central Maui that represented seven soil orders, 10 NRCS soil series, and approximately 77% of the total plantation area (Fig. 1). Soil heterogeneity across the landscape allowed for the comparison of a continuum of soil and soil properties that have experienced the same C4 grass inputs and agricultural treatment under sugarcane production for over 100 years. Conventional sugarcane production involved 2-year growth followed by harvest burn, collection of remaining stalks by mechanical ripper, deep tillage to 40 cm, no crop rotations, and little to no residue return. The sampled soils, collected from September-August 2015, thus represent a baseline of SOC after input-intensive tropical agriculture and long-term soil disturbance. Elemental analyses from this work show consistent agricultural disturbances led to degraded SOC content ranging from 0.23 to 2.91% SOC of soil mass with an average of only 1.16% SOC across all locations and depths.Figure 1Hawaiian Commercial and Sugar in central Maui with main Hawaiian Islands inset (left). Soil series identified by NRCS across HC&S fields (right) with black dots indicating 20 locations where soils were sampled to test landscape level differences in topical soil kinetics and associated soil properties under conventional sugarcane. Maps from Ref.19 created using ESRI ArcGIS with soil series data from: Soil Survey Staff, Natural Resources Conservation Service, United States Department of Agriculture, Web Soil Survey, Available online at http://websoilsurvey.nrcs.usda.gov/. Accessed [07/30/2016]19.Full size imageThe homogenized land use history allowed focused investigation of soil property effects on SOC storage across heterogenous soils (Table 1). Though soil inputs (e.g. water, nutrients, root inputs, residue removal) and disturbance regimes (e.g. burn, rip, till, compaction, no crop rotation) were consistent across the 20 field locations, average annual surface temperatures varied from 22.9 to 25.1 °C with a mean of 24.4 °C, average annual relative humidity varied from 70.4 to 79.2% with a mean of 73.4%, and average annual rainfall varied from 306 to 1493 mm with a mean of 575 mm. Gradients of rainfall, relative humidity, and elevation across the site generally increase in an east/north-east direction towards the prevailing winds and up the western slope of Haleakalā. In contrast, surface temperatures increase in the opposite direction towards Kihei and the southern tip of the West Maui Mountains.Table 1 NRCS soil classification and environmental conditions at 20 field sites.Full size tableaSoil descriptions26.bInterpolated estimates from Ref.25.Soil sampling and analysisPit locations were identified with a handheld GPS and were sampled using NRCS Rapid Carbon Assessment methods27. A total of 75 horizons were identified from the 20 selected map units to a depth of 1 m28,29. The central depth of each horizon was sampled using volumetric bulk density cores up to 50 cm. After 50 cm, a hand auger was used to check for any further horizon changes. The bulk density of horizons past 50 cm were estimated using collected soil mass and known auger size. Collected soils were air dried, processed through a 2 mm sieve, and analyzed for total C and nitrogen percent, SOC percent, soil texture, iron (Fe) and aluminum (Al) minerals, pH, cation and anion exchange capacity, extractable cations, wet and dry size classes, aggregate stability, and soil water potential at -15 kPa. Total C and nitrogen were measured by elemental analysis (Costech, ECS 4010, Valencia, CA), with SOC content determined by elemental analysis after hydrochloric acid digestion to remove carbonates. Soil texture was measured using sedimentary separation, while a 10:1 soil slurry in water was used to test soil pH. Soil pressure plates were used to measure soil water potential at -15 kPa.Fe and Al oxides were quantified in mineral phases using selective dissolutions of collected soils, including: (1) a 20:1 sodium citrate to sodium dithionite extraction, shaken 16 h, to quantify total free minerals30, (2) 0.25 M hydroxylamine hydrochloride and hydrochloric acid extraction, shaken 16 h, to quantify amorphous minerals31, and (3) 0.1 M sodium pyrophosphate (pH 10), shaken 16 h and centrifuged at 20,000g, to quantify organo-bound metals30. Extracted Fe, Al, and Si from al extractions were measured by inductively coupled plasma analysis (PerkinElmer, Optima ICP-OES, Norwalk, CT). Exploratory ratios of Fe/Al, Fe/Si, and Al/Si for the citrate/dithionite (c), hydroxylamine (h), and pyrophosphate (p) extractions were calculated. Crystalline Fe, operationally-defined as the difference between the citrate dithionite and hydroxylamine extraction, and Al + ½ Fe32 were calculated for each extraction.Plant-available phosphorus was extracted by the Olsen method using 0.5 M sodium bicarbonate adjusted to pH 8.5 and measured by continuous flow colorimetry (Hach, Lachat Quickchem 8500, Loveland, CO). Exchangeable cations (i.e. calcium, magnesium, potassium, and sodium), effective cation exchange capacity, and anion exchange capacity were measured by compulsive exchange using barium chloride and magnesium sulfate33. Cations were quantified by continuous flow colorimetry and flame-spectroscopy (Hach, Lachat Quickchem 8500, Loveland, CO). Field soils were air dried and initially passed through a 2 mm sieve before size classes of macroaggregate (2 mm – 250 µm) and microaggregate ( More

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The phototrophic species Rhodovastum atsumiense G2-11 acquired MGCs from an unknown alphaproteobacterial MTB by recent HGTIn a systematic database search for novel MGCs, we identified several orthologs of known magnetosome genes in the recently released draft genome sequence of the culturable anoxygenic phototroph Rhodovastum atsumiense G2-11 [25]. This finding was unexpected as, after isolation of G2-11 from a paddy field more than 20 years ago, no magnetosome formation has been reported [26]. Furthermore, no MTB has been identified so far among phototrophs or within the Acetobacteraceae family to which G2-11 belongs [26] (Fig. 1a).Fig. 1: Phylogeny, chromosome, and MGCs organization of G2-11.a The maximum likelihood phylogenetic tree based on ribosomal proteins demonstrates the position of G2-11 (highlighted in red) within family Acetobacteraceae (highlighted in the yellow box). The Azospirillaceae family was used as an outgroup based on the latest Alphaproteobacteria phylogeny. Branch length represents the number of base substitutions per site. Values at nodes indicate branch support calculated from 500 replicates using non-parametric bootstrap analysis. Bootstrap values 20 genes with no homology to known magnetosome genes (Fig. 1c). In contrast, the compact MGCs in G2-11 include only a few genes that could not be associated with magnetosome biosynthesis.Tetranucleotide usage patterns are frequently employed as a complementary tool to group organisms since they bear a reliable phylogenetic signal [32]. Likewise, deviations of tetranucleotide usage in a certain fragment from the flanking genome regions can indicate HGT [21]. Comparison of the z-normalized tetranucleotide frequencies of the MGCs (27.5 kb) with the flanking upstream (117.7 kb) and downstream (79.5 kb) fragments showed a considerably lower correlation between them (Pearson’s r = 0.88 with both flanking fragments) than between the flanking fragments themselves (Pearson’s r = 0.97, Fig. 1e). This indicates a significant difference in the tetranucleotide composition of the MGCs compared to the flanking genomic regions and supports a foreign origin of the magnetosome genes in G2-11 suggested by the phylogenetic analysis. Besides, the presence of a mobile element (transposase) and position of the MGCs directly downstream of a tRNA gene, a common hotspot for integration of genomic islands [33,34,35], suggests that the MGCs of G2-11 are indeed located on a genomic island, i.e., represent MAI, like in many other MTB [20, 21]. Unfortunately, the lack of other representatives of the genus Rhodovastum makes it impossible to infer whether the MAI was transferred directly to G2-11 or the last common ancestor of the genus. Nonetheless, its compact organization and conspicuous tetranucleotide usage suggest a relatively recent HGT event.G2-11 does not form magnetosomes under laboratory conditionsAlthough magnetosome genes discovered in G2-11 comply with the minimal set required for magnetosome biomineralization in MSR-1 [36], no magnetosomes have been detected in this organism. It might have several explanations: (i) the strain might switch to the magnetotactic lifestyle only under very specific, yet not tested, conditions; (ii) it once was able to synthesize magnetosomes in its natural environment but lost this ability upon subcultivation due to mutations before its characterization; (iii) the strain might naturally not exploit magnetotaxis as its genes might be non-functional or not actively expressed. To clarify which of these explanations is most likely, we first tested whether G2-11 can form magnetosomes under different laboratory conditions. To this end, the strain was cultivated photoheterotrophically, anoxic or microoxic, in a complex medium with potassium lactate and soybean peptone, as commonly used for MSR-1 (FSM) [37], as well as in minimal media with different C-sources previously shown to support growth in G2-11 (glucose, pyruvate, L-glutamine, and ethanol) [26]. All media were supplied with 50 μM ferric citrate to provide sufficient iron for magnetite biomineralization. Since magnetosome biosynthesis is possible only under low oxygen tension, aerobic chemoheterotrophic growth of G2-11 was not tested. The best growth was observed in the complex FSM medium and a minimal medium with glucose or pyruvate, whereas L-glutamine and ethanol supported only weak growth (Supplementary Fig. S3). Irrespective of the growth stage, none of the tested cultures demonstrated magnetic response as measured by a magnetically induced differential light scattering assay (Cmag) [38]. Consistently, micrographs of cells collected from stationary phase cultures did not show any magnetosome-like particles (Supplementary Fig. S3). This confirmed that G2-11 indeed cannot biosynthesize magnetosomes, at least under the conditions available for the laboratory tests. During cultivation, we also noticed that G2-11 cells did not move at any growth stage despite the initial description of this organism as motile using a single polar flagellum [26], and containing several flagellum synthesis operons and other motility-related genes. Moreover, the cells tended to adhere to glass surfaces under all tested conditions and formed a dense clumpy biofilm immersed in a thick extracellular matrix (Supplementary Fig. S3a-ii).Considering that G2-11 generally lacks magnetosomes and appears to have a stationary lifestyle, which is not consistent with magnetotaxis, we assessed whether the maintenance of MGCs comes at fitness costs for the organism. To this end, we deleted the entire region containing the magnetosome genes (in the following, referred to as the MAI region) using the genetic tools we established for G2-11 in this work (Supplementary Fig. S4a, see Materials and Methods for details). After PCR screening, replica plating test, and genome re-sequencing, two of G2-11 ΔMAI mutants were selected for further analysis (Supplementary Fig. S5). These mutants showed no significant differences in the growth behavior compared to the wildtype (WT) when incubated in minimal media supplied with acetate or pyruvate as a sole carbon source (Supplementary Fig. S4b). This finding suggests that the presence of the magnetosome genes neither provides benefits nor poses any substantial metabolic burden for G2-11, at least under the given experimental conditions.RNAseq reveals poor expression levels and antisense transcription in the MGCs of G2-11We set on to determine whether the magnetosome genes are transcribed in G2-11. To this end, we analyzed its whole transcriptome for the photoheterotrophic conditions, under which the best growth was observed, in two biological replicates. The expression levels of all the encoded genes calculated as TPM (transcripts per million) demonstrated a high correlation between the two replicates (Pearson’s r = 0.98). Most genes of the (mms6-like1)(mmsF-like1)mamH1IEKLMOH2 cluster were only poorly or not transcribed at all (Fig. 2a, Supplementary dataset). Transcription of mms6-like1, mamF-like1, mamL, mamH1, mamI, and mamK, for example, did not pass the noise background threshold (TPM ≤ 2) in both replicates and were unlikely to be expressed, whereas mamE, mamM, mamH2, feoAm, and feoBm slightly exceeded the threshold in at least one replicate and might be weakly transcribed (Fig. 2a). Although the TPM of mamO (TPM = 5.67–6.10, Supplementary dataset) exceeded the background threshold, the coverage plot reveals that the number of mapped reads sharply rises at its 3’-end, whereas the 5’-end has low read coverage (Fig. 2b). This indicates the presence of an internal transcription start site (TSS) and its associated promoter within the coding sequence of mamO instead of the full transcription of the gene. Localization of an active promoter within mamO was recently described in MSR-1, suggesting that the transcriptional organization of MGCs may be more broadly conserved across MTB than assumed previously [39].Fig. 2: Transcription of the magnetosome genes in G2-11.a Log10 of the transcript abundances for all genes in the G2-11 genome presented as TPM (transcripts per million). Red dots represent the magnetosome genes. Red rectangle shows genes with TPM below the threshold, and blue rectangle shows genes with expression levels above median. R1 and R2: biological replicates. Pearson’s r and the p value is presented on the graph. b RNAseq coverage of reads mapped on the positive (red) and negative (blue) strands of the genome in the MAI region. The gray balk shows the gene map: genes encoded on the negative strand are colored in black, on the positive – in green. Red arrows indicate the anti-sense transcription in the mamPAQRBST operon. Green arrows indicate the intragenic TSS within mamO. TSS are indicated with dashed lines and black arrowheads that show the direction of transcription.Full size imageTranscription of genes within the mag123, (mms6-like2)(mmsF-like2), and mamAPQRBST clusters significantly exceeded the threshold, with the expression levels of mag1, mamT, and mamS being above the overall median. At the same time, antisense transcription was detected in the mamAPQRBST region, with the coverage considerably exceeding the sense transcription (Fig. 2b). This antisense RNA (asRNA) likely originated from a promoter controlling the tRNA gene positioned on the negative strand downstream of mamT. Such long asRNAs have the potential to interfere with sense transcripts, thereby significantly decreasing the expression of genes encoded on the opposite strand [40].In summary, the RNAseq data revealed extremely low or lack of transcription of several genes that are known to be essential for magnetosome biosynthesis (mamL, mamI, mamM, mamE, and mamO) [27, 41]. Additionally, the detected antisense transcription can potentially attenuate expression of the mamAPQRBST cluster that also comprises essential genes, i.e., mamQ and mamB. Although other factors, like the absence of several accessory genes mentioned above and the potential accumulation of point mutations, might also be involved, the lack or insufficient transcription of the essential magnetosome genes appears to be the primary reason for the absence of magnetosome biosynthesis in G2-11.Magnetosome proteins from G2-11 are functional in a model magnetotactic bacteriumAlthough visual inspection of the G2-11 magnetosome genes did not reveal any frameshifts or other apparent mutations, accumulation of non-obvious functionally deleterious point substitutions in the essential genes could not be excluded. Therefore, we next tested whether at least some of the magnetosome genes from G2-11 still encode functional proteins that can complement isogenic mutants of the model magnetotactic bacterium MSR-1. In addition, we analyzed the intracellular localization of their products in both MSR-1 and G2-11 by fluorescent labeling.One of the key proteins for magnetosome biosynthesis in MSR-1 is MamB, as its deletion mutant is severely impaired in magnetosome vesicle formation and is entirely devoid of magnetite crystals [42, 43]. Here, we observed that expression of MamB[G2-11] partially restored magnetosome chain formation in MSR-1 ΔmamB (Fig. 3a, b-i, b-ii). Consistently, MamB[G2-11] tagged with mNeonGreen (MamB[G2-11]-mNG) was predominantly localized to magnetosome chains in MSR-1, suggesting that the magnetosome vesicle formation was likely restored to the WT levels (Fig. 3b-iii).Fig. 3: Genetic complementation and intracellular localization of magnetosome proteins from G2-11 in MSR-1 isogenic mutants.a TEM micrograph of MSR-1 wildtype (WT). b MSR-1 ΔmamB::mamB[G2-11]. b-i TEM micrograph and b-ii magnetosome chain close-up; b-iii) 3D-SIM Z-stack maximum intensity projection of MSR-1 ΔmamB::mamB[G2-11]-mNG. c MSR-1ΔmamQ::mamQ[G2-11]. c-i TEM micrograph and c-ii close-up of the particles; c-iii 3D-SIM Z-stack maximum intensity projection. d MSR-1 ΔmamK::mamK[G2-11]. d-i TEM micrograph of MSR-1 ΔmamK; d-ii TEM micrograph of MSR-1 ΔmamK::mamK[G2-11]; d-iii 3D-SIM Z-stack maximum intensity projection of MSR-1 ΔmamK::mNG-mamK[G2-11]. e MSR-1 ΔmamKY::mamK[G2-11]. e-i-ii Representative cells of MSR-1 ΔmamKY mutant showing examples of a short chain, cluster (e-i), and ring-shaped chain (e-ii); (e-iii) TEM micrograph of MSR ΔmamKY::mamK[G2-11] mutant showing the complemented phenotype; e-iv distribution of cells with different phenotypes in the populations of MSR-1 ΔmamKY and MSR-1 ΔmamKY::mamK[G2-11] mutants (N  > 50 cells for each strain population); e-v 3D-SIM Z-stack maximum intensity projection of MSR-1 ΔmamKY::mNG-mamK[G2-11]. f MSR-1 ΔmamJ::mamJ-like[G2-11]. f-i TEM micrograph of MSR-1 ΔmamJ; f-ii TEM micrograph of MSR-1 ΔmamJ::mamJ-like[G2-11]; f-iii 3D-SIM Z-stack maximum intensity projection of MSR-1 ΔmamJ::mamJ-like[G2-11]-gfp. g MSR-1 ΔF3::mmsF-like1[G2-11] and ΔF3::mmsF-like2[G2-11]. g-i TEM micrograph of MSR-1 ΔF3; g-ii TEM micrograph of MSR-1 ΔF3::mmsF-like1[G2-11]; g-iii TEM micrograph of MSR-1 ΔF3::mmsF-like2[G2-11]; g-iv magnetosome diameter distribution in MSR-1 ΔF3 and the mutants complemented with mmsF-like1/mmsF-like2. Asterisks indicate points of significance calculated using Kruskal–Wallis test (****p 50 cells for each of two randomly selected insertion mutants MSR-1 ΔmamKY::mamK[G2-11] revealed that the long magnetosome chains were restored in 35-40% of the population (Fig. 3e-iv). Of note, mNG-MamK[G2-11] formed slightly shorter filaments in MSR-1 ΔmamKY than in ΔmamK, which were also characteristically displaced to the outer cell curvature due to the lack of mamY [46] (Fig. 3e-v).MamJ attaches magnetosomes to the MamK filament in MSR-1, mediating their chain-like arrangement. Elimination of mamJ disrupts this linkage, causing magnetosomes to aggregate owing to magnetic interactions [47] (Fig. 3f-i). In MSR-1, MamJ is encoded within the mamAB operon, between mamE and mamK. Within the (mms6-like1)(mmsF-like1)mamH1IEKLMOH2 cluster of G2-11, there is an open reading frame (ORF) encoding a hypothetical protein that is located in a syntenic locus (Fig. 1c). Although the hypothetical protein from G2-11 and MamJ from MSR-1 differ considerably in length (563 vs. 426 aa), share only a low overall sequence similarity (31%), and are not identified as orthologues by reciprocal blast analyses, multiple sequence alignments revealed a few conserved amino acids at their N- and C-termini (Supplementary Fig. S6). Moreover, in both proteins, these conserved residues are separated by a large region rich in acidic residues (pI 3.3 and 3.2) suggesting that the G2-11 protein might be a distant MamJ homolog. To test if it implements the same function as MamJ, we transferred this gene to MSR-1 ΔmamJ. Interestingly, it indeed restored chain-like magnetosome arrangement, which, however, often appeared as closed rings rather than linear chains (Fig. 3f-ii). Despite this difference, it indicated the ability of the hypothetical protein (hereafter referred to as MamJ-like[G2-11]) to attach magnetosomes to MamK, suggesting that in the native context, it can have a function identical to MamJ. Consistently, its fluorescently labeled version was often observed in ring-like structures within the cytoplasm of MSR-1 ΔmamJ, suggesting that it is indeed localized to magnetosomes (Fig. 3f-iii).In magnetospirilla, magnetosome proteins MmsF, MamF, and MmxF share an extensive similarity. Their individual and collective elimination gradually reduces the magnetite crystal size and disrupts the chain formation in MSR-1 (Fig. 3g-i; Paulus, manuscript in preparation). The MAI of G2-11 includes two genes, whose products have high similarity to these proteins, designated here as MmsF-like1[G2-11] and MmsF-like2[G2-11]. Expression of each of them in the MSR-1 ΔmmsFΔmamFΔmmxF triple mutant (ΔF3) partially restored the magnetosome size and led to the formation of short magnetosome chains in MSR ΔF3::mmsF-like1[G2-11] (Fig. 3g-ii) or clusters in MSR-1 ΔF3::mmsF-like2[G2-11] (Fig. 3g-iii, iv). Consistently, fluorescently tagged mNG-MmsF-like1[G2-11] and mNG-MmsF-like2[G2-11] localized to magnetosomes in the pattern resembling that in the TEM micrographs of the complemented corresponding mutants (Fig. 3g-v, vii), or were perfectly targeted to the magnetosome chains in MSR-1 WT (Fig. 3g-vi, viii).In G2-11, MamB[G2-11]-mNG, mNG-MamQ[G2-11], MamJ-like[G2-11]-GFP, mNG-MmsF-like1[G2-11], and mNG-MmsF-like2[G2-11] were patchy-like or evenly distributed in the inner and intracellular membranes (Supplementary Fig. S7). No linear structures that would indicate the formation of aligned magnetosome vesicles were observed in these mutants. As expected, mNG-MamK[G2-11] formed filaments in G2-11 (Supplementary Fig. S7c).Expression of MamM, MamO, MamE, and MamL failed to complement the corresponding deletion mutants of MSR-1 (not shown). Although detrimental mutations in the genes cannot be excluded, this result can be attributed to the lack of their native, cognate interaction partners, likely due to the large phylogenetic distances between the respective orthologues.Transfer of MGCs from MSR-1 endows G2-11 with magnetosome biosynthesis that is rapidly lost upon subcultivationHaving demonstrated the functionality of several G2-11 magnetosome genes in the MSR-1 background, we wondered whether, conversely, the G2-11 background is permissive for magnetosome biosynthesis. To this end, we transferred the well-studied MGCs from MSR-1 into G2-11, thereby mimicking an HGT event under laboratory conditions. The magnetosome genes from MSR-1 were previously cloned on a single vector pTpsMAG1 to enable the one-step transfer and random insertion into the genomes of foreign organisms [23]. Three G2-11 mutants with different positions of the integrated magnetosome cassette were incubated under anoxic phototrophic conditions with iron concentrations (50 μM) sufficient for biomineralization in the donor organism MSR-1. The obtained transgenic strains indeed demonstrated a detectable magnetic response (Cmag = 0.38 ± 0.11) [38], and TEM confirmed the presence of numerous electron-dense particles within the cells (Fig. 4), which, however, were significantly smaller than magnetosome crystals of MSR-1 (ranging 18.5 ± 4.3 nm to 19.9 ± 5.0 nm in three G2-11 MAG insertion mutants vs 35.4 ± 11.5 nm in MSR-1 WT, Fig. 4b) and formed only short chains or were scattered throughout the cells (Fig. 4a, c-i). Mapping of the particle elemental compositions with energy-dispersive X-ray spectroscopy (EDS) in STEM mode revealed iron- and oxygen-dominated compositions, suggesting they were iron oxides. High-resolution TEM (HRTEM) images and their FFT (Fast Fourier Transform) patterns were consistent with the structure of magnetite (Fig. 4c). Thus, G2-11 was capable of genuine magnetosome formation after acquisition of the MGCs from MSR-1.Fig. 4: Magnetosome biosynthesis by G2-11 upon transfer of the MGCs from MSR-1.a A cell with magnetosomes (i) and a close-up of the area with magnetosome chains (ii). Scale bars: 1 µm. b Violin plots displaying magnetosome diameter in three MAG insertion mutants of G2-11 in comparison to MSR-1. Asterisks indicate points of significance calculated using the Kruskal–Wallis test (**** designates p  More

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