Abstract
Understanding how high species diversity is maintained in natural bacterial communities is a central question in microbial ecology. Due to the versatile heterotrophic capacities of bacteria and the rich nutrients released by deceased bacterial cells, necromass recycling plays an important role in sustaining bacterial growth. Such nutrient cycling within communities can provide additional resource niches for bacteria, but its potential effects on bacterial diversity maintenance have been neglected. Here we conducted two independent experiments and studied the assembly of 276 soil-derived bacterial communities sustained by a wide range of bacterial necromass combinations, from single-species necromass to combinations of up to nearly 1,000 species. Our results highlight the existence of a species-rich bacterial necrobiome in soil. We found that the composition of necromass-decomposing communities was determined by the various organic compounds in the different necromass combinations, and the increases in necromass-producing species constantly promoted species diversity of necromass-decomposing communities. Moreover, the average niche breadth and overlap of coexisting necromass-decomposing species in utilizing distinct single-species necromass decreased with increases in necromass diversity, supporting the hypothesis of resource partitioning in utilizing different single-species necromass. Our study provides insights into diversity maintenance in bacterial communities from a perspective of internal nutrient cycling.
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Data availability
Raw data of 16S rRNA gene sequences are deposited at NCBI SRA under BioProject PRJNA1283958. LC–MS data and supplementary figure source data are included in Supplementary Data provided with this paper. Source data are provided with this paper.
Code availability
The R scripts used for data analyses in this study are publicly available in GitHub at https://github.com/yiqiSCNU/Bacterial-necromass-recycling-experiment (ref. 83).
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (32371597). Y.-Q.H. was supported by the National Natural Science Foundation of China (32271600).
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X.-F.Z. designed the study. X.-F.Z., B.-H.L. and J.-Y.C. performed the experiment. Y.-Q.H. performed data analyses and took the lead in writing the manuscript. X.-F.Z. supervised the project. W.-S.S. provided critical feedback. All authors helped shape the analyses and manuscript.
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Extended data
Extended Data Fig. 1 Metric multidimensional scaling ordinations of necromass-decomposing communities (NDCs) across six transfers by principal coordinate analyses (PCoA).
Seven necromass treatments (one at each combination level, except two at the combination level 1) were randomly chosen. The compositional changes of NDCs (n = 6 replicates) during six transfers in the seven necromass combination treatments are shown by PCoA separately. Each point represents an experimental NDC. Distances among communities represent Bray-Curtis dissimilarities. The communities are colored based on the sampling time. NDCs in all seven necromass treatments showed no significant differences in community composition between the fifth and sixth transfers (PERMANOVA for each treatment separately, Supplementary Table 2).
Source data
Extended Data Fig. 2 Metric multidimensional scaling ordinations of experimental bacterial communities (n = 257) by principal coordinate analyses (PCoA) for the necromass combination experiment.
Each point represents an experimental community. Distances among communities represent Bray-Curtis dissimilarities. The communities are displayed together or separately at each combination level for clarity. The communities are colored based on the combination levels or specific necromass combination treatments at each combination level.
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Extended Data Fig. 3 The correlations between the compositional distances among NDCs (n = 257) and the compositional distances, phylogenetic distances, functional distances among corresponding NPS combinations in the necromass combination experiment.
a, The compositional distances were measured as Bray-Curtis dissimilarities among NDCs or NPS combinations. b, The phylogenetic distances were measured as UniFrac dissimilarities. c, The functional distances were measured as Bray-Curtis dissimilarities of the predicted KEGG orthologies. The dark grey smoothing curves represent generalized additive model (GAM) fits. The statistics of the significant positive correlations are provided in the bottom of panels (two-sided Mantel tests, permutations = 999).
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Extended Data Fig. 4 Metabolomic profiling reveals compositional differences in necromass and differential necromass utilization patterns across twelve focal bacterial species.
a, Standardized metabolite abundance in the twelve single-species necromass media. Mean abundance values of five replicates per single-species necromass were log10-transformed, followed by z-score standardization. A positive (red) or negative (blue) value indicates higher or lower abundance relative to the interspecies mean. In total of 107 metabolites are displayed. These metabolites exhibited significant interspecies variations (two-sided Kruskal-Wallis test, FDR < 0.05), with maximum abundance differences exceeding 200 times between necromass-producing species (NPS). b, Log10-fold changes of metabolite abundance in spent necromass media compared to the twelve-species necromass medium control. Log10-fold changes were calculated based on the mean abundance of metabolites across five replicates in the spent culture of each species and twelve-species necromass medium. A positive (red) or negative (blue) value indicates production or consumption of corresponding compound in the twelve-species necromass medium. Deep blue represents metabolites were depleted below the limit of detection. In total of 123 consumed metabolites are displayed. These consumed metabolites showed significantly differential depletion across consumption treatments (two-sided Kruskal-Wallis test, FDR < 0.05), with maximum depletion exceeding 90% relative to control medium. Metabolites are classified by compound class, and focal species are annotated by phylogenetic order in both heatmaps. c, Principal Component Analysis (PCA) for metabolomic profiles of spent cultures (n = 60). Each point represents a spent culture sample. Dissimilarities of metabolomic profile among samples were quantified using Euclidean distances. Samples are colored based on the consumer bacterial species. Statistics of one-sided PERMANOVA are provided in the bottom of panel.
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Extended Data Fig. 5 Pairwise relationships and distributions of key variables in the necromass combination experiment.
This scatterplot matrix characterizes interdependencies among five key variables: the number of NPS in the combinations (richness.NPS, n = 43), mean phylogenetic distance of NPS combinations (mpd.NPS, n = 43), the predicted number of KEGG orthologies of NPS combinations (KO.richness.NPS, n = 43), the number of metabolomic features of NPS combinations (MF.richness.NPS, n = 43) and richness of NDCs (richness.NDC, n = 257). Diagonal elements display kernel density estimates of each variable. Lower-triangular panels illustrate pairwise correlations through scatterplots with locally weighted smoothing curves (red lines). Pearson correlation coefficient (r) and significance value (p) from two-sided test are provided in each panel. Note that our experimental design of necromass combinations decoupled mpd.NPS from the number of NPS across 2-12 NPS levels (r = −0.043, p = 0.56). However, the mean phylogenetic distance is inherently zero for all single-species treatments (NPS = 1). Consequently, inclusion of the single-species treatments introduced a forced positive correlation between mpd.NPS and richness.NPS as observed in the upper left panel.
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Extended Data Fig. 6 Species loss and preservation patterns across necromass utilization niche breadths in the necromass combination experiment.
a, Comparisons of the numbers of lost (red circle) and preserved (cyan circle) necromass-decomposing species (NDS) in multi-species necromass treatments at each necromass combination level. NDS were categorized into common and rare species using a 0.1% relative abundance threshold. The necromass utilization niche breadths of NDS were measured as their occurrence number in the twelve single-species necromass treatments. NDS with niche breadths spanning 1 to 12 represented a specialist-to-generalist continuum in single-species necromass utilization. The NDS sustained by the component single-species necromass, but not detected in the corresponding multi-species necromass treatments were defined as the lost species. The preserved species were defined as those sustained by the component single-species necromass, and also present in the corresponding multi-species necromass treatments. Both the lost and preserved species were grouped based on their niche breadths. One data point represents one multi-species necromass treatment. The numbers of rare species are shown in log10 scale for clarity. b, The proportion of preserved species increased linearly with necromass utilization niche breadths. The proportion of preserved species was defined as the number of preserved species divided by the total species (preserved + lost species) within each niche breadth group. The statistics of linear regressions are provided at the top of panels (n = 372).
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Extended Data Fig. 7 The relative abundance of major phyla.
a, The major phyla in the original soil bacterial community, and necromass-decomposing communities (NDCs) at the end of necromass combination experiment. b, The major phyla in the necromass-producing communities (NPCs) and NDCs at the end of the species-rich necromass experiment.
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Extended Data Fig. 8 The positive correlations between the compositional distances among NDCs (n = 18) and the compositional distances, phylogenetic distances, functional distances among corresponding NPCs (n = 18) in the species-rich necromass experiment.
a, The compositional distances were measured as Bray-Curtis dissimilarities among NDCs or NPCs. b, The phylogenetic distances were measured as UniFrac dissimilarities. c, The functional distances were measured as Bray-Curtis dissimilarities of the predicted KEGG orthologies. The grey lines represent linear regression fits. The statistics of the significant positive correlations are provided in the bottom of panels (two-sided Mantel tests, permutations = 999).
Source data
Extended Data Fig. 9 Pairwise relationships and distributions of key variables in the species-rich necromass experiment.
This scatterplot matrix characterizes interdependencies among four key variables: specie richness of NPCs (richness.NPC, n = 18), mean phylogenetic distance of NPCs (mpd.NPC, n = 18), the predicted number of KEGG orthologies of NPCs (KO.richness.NPC, n = 18), and richness of NDCs (richness.NDC, n = 18). Diagonal elements display kernel density estimates of each variable. Lower-triangular panels illustrate pairwise correlations through scatterplots with linear regressions (red lines). Pearson correlation coefficient (r) and significance value (p) from two-sided test are provided in each panel.
Source data
Extended Data Fig. 10 The relationships between the relative abundance (on a logarithmic scale) of the twelve focal necromass-producing species (NPS, A – L) in the necromass-decomposing communities (NDCs, n = 257) and their necromass proportions in the corresponding necromass combinations.
Take species A for example, its necromass proportion in the treatment A is 12/12, in the treatment AB is 6/12, in the treatment BD is 0/12. The lower and upper ends of the boxes represent 25% and 75% of the range, respectively; lines in the boxes indicate medians; and whiskers represent ± 1.5 × the interquartile range (IQR, defined as the upper quartile minus the lower quartile). The statistics of Pearson correlation analyses (two-sided tests) are provided in the top of the panels. Species K was not detected in any NDCs. For 8 out of 12 species, there was no significant positive correlation between their relative abundance and necromass proportions. And for 3 (C, I and K) out of 12 species, their relative abundance was significantly lower than 10−4 in their corresponding single-species necromass treatments. Given that the degradation rates of DNA from different species are the same, we speculated that there was barely residual DNA derived from the necromass of focal NPS in the microcosms after 2 days of decomposition. We also observed that 11 out of 12 species had high relative abundance in the treatment where their necromass proportions were zero. Thus, these NPS were also necromass-decomposing species in our experimental communities. In summary, these eleven focal species in the NDCs were enriched from the soil bacterial community, rather than the false-positive results due to the residual DNA within the necromass nutrients. These results indicated that the NPS could utilize necromass nutrients from both other species and their own. In most cases, they achieved higher abundance by utilizing necromass nutrients from other species rather than their own, and they were also not the best decomposer of their own necromass.
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Hao, YQ., Li, BH., Chen, JY. et al. Bacterial necromass recycling promotes diversity maintenance in bacterial communities via resource partitioning.
Nat Ecol Evol (2026). https://doi.org/10.1038/s41559-025-02967-2
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DOI: https://doi.org/10.1038/s41559-025-02967-2
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