Soil Microbial Networks Shift Across a High-Elevation Successional Gradient

Farrer, Emily C.; Porazinska, Dorota L.; Spasojevic, Marko J.; King, Andrew J.; Mesquita, Clifton P. Bueno de; Sartwell, Samuel A.; Smith, J. A.; White, C. T.; Schmidt, Steven K.; Suding, Katharine N.

doi:10.3389/fmicb.2019.02887

Cited by 16 publications

(9 citation statements)

References 96 publications

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“…Intriguingly and contrary to the previous conclusion that temperature had a stimulating effect on the microbes (Farrer et al, 2019), we found that the relative abundances of most of the target genes were higher in the nongrowing (winter) than the growing (summer) season (Figure 4; Table S5). Soil temperature was also not significantly correlated with P availability across sites and seasons (Figure S3).…”

Section: Discussioncontrasting

confidence: 99%

“…On the one hand, wetland salinization strongly affected the physicochemical characteristics of the soil water (Table S3), which can induce a strong selection pressure on soil microbial communities, thereby excluding many microbes from the network (Ratzke et al, 2020). On the other hand, previous studies have reported that high microbial diversity generally implies that rich microbial communities simultaneously compete for the same resources and energy within their habitats, which is accompanied by low network complexity (Farrer et al, 2019;Gao et al, 2022), consistent with the high microbial diversity we observed in the brackish wetland (Figure 2).…”

Section: Response Of P-cycling Microbial Genes To Salinitymentioning

confidence: 99%

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Moderate salinity improves the availability of soil P by regulating P‐cycling microbial communities in coastal wetlands

Sardans

et al. 2022

Global Change Biology

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Accelerated sea-level rise is expected to cause the salinization of freshwater wetlands, but the responses to salinity of the availability of soil phosphorus (P) and of microbial genes involved in the cycling of P remain unexplored. We conducted a field experiment to investigate the effects of salinity on P cycling by soil microbial communities and their regulatory roles on P availability in coastal freshwater and brackish wetlands. Salinity was positively correlated with P availability, with higher concentrations of labile P but lower concentrations of moderately labile P in the brackish wetland.The diversity and richness of microbial communities involved in P cycling were higher in the brackish wetland than the freshwater wetland. Salinity substantially altered the composition of the P-cycling microbial community, in which those of the brackish wetland were separated from those of the freshwater wetland. Metagenomic sequence analysis indicated that functional genes involved in the solubilization of inorganic P and the subsequent transport and regulation of P were more abundant in coastal soils.The relative abundances of most of the target genes differed between the wetlands, with higher abundances of P-solubilization (gcd and ppa) and -mineralization (phoD, phy, and ugpQ) genes and lower abundances of P-transport genes (pstB, ugpA, ugpB, ugpE, and pit) in the brackish wetland. A significant positive correlation between the concentration of labile P and the abundances of the target genes suggested that salinity may, at least in part, improve P availability by regulating the P-cycling microbial community. Our results suggest that the P-cycling microbial community abundance and P availability respond positively to moderate increases in salinity by promoting the microbial solubilization and mineralization of soil P. Changes in microbial communities and microbially mediated P cycling may represent microbial strategies to adapt to moderate salinity levels, which in turn control soil function and nutrient balance.

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Section: Discussioncontrasting

confidence: 99%

Section: Response Of P-cycling Microbial Genes To Salinitymentioning

confidence: 99%

Moderate salinity improves the availability of soil P by regulating P‐cycling microbial communities in coastal wetlands

Sardans

et al. 2022

Global Change Biology

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“…3; Table 3). The main local filters were spatial distance and elevation, which together explained 46.8% of the total variation, the same as found in previous biogeographic studies (Fierer and Jackson 2006;Pellissier et al 2014;Wang et al 2017;Farrer et al 2019), with a secondary effect of the season (Goss-Souza et al 2017;Ma et al 2017), biopores, an abiotic soil physical factor. The average weighted degree was the major biotic filter of bacterial communities at the local scale (11.9%), corroborating the findings of a biogeographic study of bacterial communities in paddy soils at a continental 32 scale (Gao et al 2019).…”

Section: Drivers Of Bacterial Assembly Patterns and Processes Across ...supporting

confidence: 81%

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

Goss‐Souza

Tsai

Rodrigues

et al. 2022

Antonie van Leeuwenhoek

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Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totalizing 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world's largest and most threatened hotspots of biodiversity. We observed no significant shifts in alpha diversity due to land-use change.Meanwhile, pairwise beta diversities and distance decays were lower in pastures than those observed for forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal process were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical/evolutionary contingencies and the interactions among taxa (i.e. co-occurrence patterns) than the land-use change itself.

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“…However, associations between Dehalococcoidia and sulfate‐reducing bacteria in Deltaproteobacteria were identified in deep sediments, suggesting that sulphate‐reducing activity may enhance dechlorination by Dehalococcoidia (May et al, 2008). Other studies have suggested that carbon inputs and shifts in carbon resource increased network complexity (Farrer et al, 2019; Shi et al, 2016), which could possibly explain the drastic increase of interactions in the network of 30–90 cm, as increased TOC and distinct δ 13 C was detected at ~50 cm. These results indicated that terrestrial inputs may also influence the structure of microbial co‐occurrence networks.…”

Section: Discussionmentioning

confidence: 91%

Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments

et al. 2021

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Microbial abundance and community composition in marine sediments have been widely explored. However, high‐resolution vertical changes of benthic microbial diversity and co‐occurrence patterns are poorly described. The ecological contributions of abundant and rare species in sediments also remain largely unknown. Here, by analysing microbial populations at 14 depth layers of 10 subseafloor sediment cores (water depth 1,250–3,530 m) obtained in the South China Sea, we provided the vertical profiles of microbial β‐diversity and co‐occurrence influenced by subcommunities of different abundance. These 134 sediment samples were clustered into four groups according to sediment depth (1–2, 6–10, 30–90 and 190–790 cm) with obvious shifts in microbial community compositions. The vertical succession of microorganisms was consistent with redox zonation and influenced by terrestrial inputs. Partitioning of vertical β‐diversity showed extremely high species replacement between deep layers and the surface layer, indicating selection‐induced loss of rare species and dispersal of dormant cells and spores. By contrast, for horizontal β‐diversity, richness of rare species became increasingly significant in deep sediments. Accompanying this β‐diversity profile were clear changes in the association pattern, with microorganisms being less connected in deeper sediment layers, probably reflecting reduced syntrophic interactions. Rare species accounted for an indispensable proportion in the co‐occurrence network, and tended to form complex “small worlds.” The rare subcommunity also responded differently to various environmental factors compared with the abundant subcommunity. Our findings expand current knowledge on vertical changes of marine benthic microbial diversity and their association patterns, emphasizing the potential roles of rare species.

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Soil Microbial Networks Shift Across a High-Elevation Successional Gradient

Cited by 16 publications

References 96 publications

Moderate salinity improves the availability of soil P by regulating P‐cycling microbial communities in coastal wetlands

Moderate salinity improves the availability of soil P by regulating P‐cycling microbial communities in coastal wetlands

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments

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