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Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13 C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

The aim of this study was to gain understanding of the carbon flow from the roots of a genetically modified (GM) amylopectin-accumulating potato (Solanum tuberosum) cultivar and its parental isoline to the soil fungal community using stable isotope probing (SIP). The microbes receiving 13C from the plant were assessed through RNA/phospholipid fatty acid analysis with stable isotope probing (PLFA-SIP) at three time-points (1, 5 and 12 d after the start of labeling). The communities of Ascomycota, Basidiomycota and Glomeromycota were analysed separately with RT-qPCR and terminal restriction fragment length polymorphism (T-RFLP). Ascomycetes and glomeromycetes received carbon from the plant as early as 1 and 5 d after labeling, while basidiomycetes were slower in accumulating the labeled carbon. The rate of carbon allocation in the GM variety differed from that in its parental variety, thereby affecting soil fungal communities. We conclude that both saprotrophic and mycorrhizal fungi rapidly metabolize organic substrates flowing from the root into the rhizosphere, that there are large differences in utilization of root-derived compounds at a lower phylogenetic level within investigated fungal phyla, and that active communities in the rhizosphere differ between the GM plant and its parental cultivar through effects of differential carbon flow from the plant.

Understanding how altered soil organic carbon (SOC) availability affects microbial communities and their function is imperative in predicting impacts of global change on soil carbon (C) storage and ecosystem function. However, the response of soil microbial communities and their function to depleted C availability in situ is unclear. We evaluated the role of soil C inputs in controlling microbial biomass, community composition, physiology, and function by (1) experimentally excluding plant C inputs in situ for 9 yr in four temperate forest ecosystems along a productivity gradient in Oregon, USA; and (2) integrating these findings with published data from similar C-exclusion studies into a global meta-analysis. Excluding plant C inputs for 9 yr resulted in a 13% decrease in SOC across the four Oregon sites and an overall shift in the microbial community composition, with a 45% decrease in the fungal : bacterial ratio and a 13% increase in Gram-positive : Gram-negative bacterial ratio. Although gross N mineralization decreased under C exclusion, decreases in gross N immobilization were greater, resulting in increased net N mineralization rates in all but the lowest-productivity site. Microbial biomass showed a variable response to C exclusion that was method dependent; however, we detected a 29% decrease in C-use efficiency across the sites, with greater declines occurring in less-productive sites. Although extracellular enzyme activity increased with C exclusion, C exclusion resulted in a 31% decrease in microbial respiration across all sites. Our meta-analyses of published data with similar C-exclusion treatments were largely consistent with our experimental results, showing decreased SOC, fungal : bacterial ratios, and microbial respiration, and increased Gram-positive : Gram-negative bacterial ratio following exclusion of C inputs to soil. Effect sizes of SOC and respiration correlated negatively with the duration of C exclusion; however, there were immediate effects of C exclusion on microbial community composition and biomass that were unaltered by duration of treatment. Our field-based experimental results and analyses demonstrate unequivocally the dominant control of C availability on soil microbial biomass, community composition, and function, and provide additional insight into the mechanisms for these effects in forest ecosystems.

Although soil microbial communities are known to play crucial roles in the cycling of nutrients in forest ecosystems and can vary by plant species, how microorganisms respond to the subtle gradients of plant genetic variation is just beginning to be appreciated. Using a model Populus system in a common garden with replicated clones of known genotypes, we evaluated microbial biomass and community composition as quantitative traits. Two main patterns emerged. (1) Plant genotype influenced microbial biomass nitrogen in soils under replicated genotypes of Populus angustifolia, F₁, and backcross hybrids, but not P. fremontii. Genotype explained up to 78% of the variation in microbial biomass as indicated by broad-sense heritability estimates (i.e., clonal repeatability). A second estimate of microbial biomass (total phospholipid fatty acid) was more conservative and showed significant genotype effects in P. angustifolia and backcross hybrids. (2) Plant genotype significantly influenced microbial community composition, explaining up to 70% of the variation in community composition within P. angustifolia genotypes alone. These findings suggest that variation in above- and belowground traits of individual plant genotypes can alter soil microbial dynamics, and suggests that further investigations of the evolutionary implications of genetic feedbacks are warranted.

Soil microbes are crucial for regulating biogeochemical cycles and maintaining forest ecosystem sustainability; however, the understanding of microbial communities and enzyme activity under natural and plantation forests in plateau regions remains limited. Using soil samples from 15-, 30-, and 50-year-old Picea crassifolia plantations and a natural forest (NF) in eastern Qinghai, China, this study assessed physicochemical properties, microbial communities, and enzyme activity across three soil layers. Microbial composition was characterized using the phospholipid fatty acid (PLFA) method, which is sensitive to structural changes. The PLFAs of bacteria, fungi, and actinomycetes accounted for 58.31%–74.20%, 8.91%–16.83%, and 3.41%–10.41% of the total PLFAs in all forests, respectively. There were significant differences between the NF and plantations, with the NF exhibiting higher PLFA abundance and enzyme activities than plantations, except for fungal PLFAs. PLFAs in plantations increased with the plantation age. However, the fungi-to-bacteria ratio was lower in the NF than in plantations. Finally, a redundancy analysis revealed that soil properties influence microbial composition and enzyme functionality significantly. These findings highlight the influence of stand age on microbial communities and structure, offering valuable insights for forest management practices aimed at conserving natural forests.

Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10 g kg⁻¹ soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp™ method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7 %, while soil water status explained 7.5 and 29.1 %, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity.

In this study, we report on the bacterial diversity and their functional properties prevalent in tea garden soils of Assam that have low pH (3.8–5.5). Culture-dependent studies and phospholipid fatty acid analysis revealed a high abundance of Gram-positive bacteria. Further, 70 acid-tolerant bacterial isolates characterized using a polyphasic taxonomy approach could be grouped to the genus Bacillus , Lysinibacillus , Staphylococcus , Brevundimonas , Alcaligenes , Enterobacter , Klebsiella , Escherichia , and Aeromonas . Among the 70 isolates, 47 most promising isolates were tested for their plant growth promoting activity based on the production of Indole Acetic Acid (IAA), siderophore, and HCN as well as solubilization of phosphate, zinc, and potassium. Out of the 47 isolates, 10 isolates tested positive for the entire aforesaid plant growth promoting tests and further tested for quantitative analyses for production of IAA, siderophore, and phosphate solubilization at the acidic and neutral condition. Results indicated that IAA and siderophore production, as well as phosphate solubilization efficiency of the isolates decreased significantly ( P  ≤ 0.05) in the acidic environment. This study revealed that low soil pH influences bacterial community structure and their functional properties.

In boreal peatlands, the aboveground (plant) and belowground (microbial) communities are acutely linked because the whole soil profile is partially decomposed plant matter (peat), and dictates the nutrients available to the belowground system. We characterized the aboveground and belowground communities in two boreal peatlands: a Sphagnum dominated fen and a Carex-dominated fen. We link the plant and microbial communities by observing plant, litter and peat carbon and nitrogen values. The Sphagnum-dominated fen had greater plant diversity but provided low quality litter inputs (high carbon:nitrogen) that formed peat and that corresponded with greater fungi:bacteria and Gram-positive:Gram-negative bacteria microbial community compared to the Carex-dominated fen. The higher quality plant inputs in the Carex-dominated fen supported a 5 × greater microbial biomass that was also 2 × more active (as measure by CO₂ production). In this approach we highlight that peatlands and their component plant and microbial communities play-out along a common resource-spectrum that dictates ‘fast’ vs ‘slow’ carbon and nutrient cycling (i.e., a plant–soil interaction spectrum) that can, in turn, affect carbon storage potential. As peatland plant community composition is predicted to shift and decomposition rates are expected to increase under climate change, our work highlights the importance of understanding plant–soil microbial interactions.

Salt marshes exist at the interface of the marine and the terrestrial system. Shore height differences and associated variations in inundation frequency result in altered abiotic conditions, plant communities, and resource input into the belowground system. These factors result in three unique zones, the upper salt marsh (USM), the lower salt marsh (LSM), and the pioneer zone (PZ). Marine detritus, such as micro‐ and macroalgae, is typically flushed into the PZ daily, with storm surges moving both salt marsh detritus and marine detritus into higher salt marsh zones. Microbial assemblages are essential for the decomposition of organic matter and have been shown to sensitively respond to changes in abiotic conditions such as oxygen supply and salinity. However, temporal and spatial dynamics of microbial communities of Wadden Sea salt marshes received little attention. We investigated the dynamics of soil microbial communities across horizontal (USM, LSM, and PZ), vertical (0–5 and 5–10‐cm sediment depth), and temporal (spring, summer, and autumn) scales in the Wadden Sea salt marsh of the European North Atlantic coast using phospholipid fatty acid (PLFA) analysis. Our results show strong spatial dynamics both among salt marsh zones and between sediment depths, but temporal dynamics to be only minor. Despite varying in space and time, PLFA markers indicated that bacteria generally were the dominant microbial group across salt marsh zones and seasons, however, their dominance was most pronounced in the USM, whereas fungal biomass peaked in the LSM and algal biomass in the PZ. Only algal markers and the stress marker monounsaturated to saturated fatty acid ratio responded to seasonality. Overall, therefore, the results indicate remarkable temporal stability of salt marsh microbial communities despite strong variability in abiotic factors. We investigated salt marsh soil microbial community dynamics across spatial scales—shore height and soil depth—as well as temporal scales (spring, summer, and autumn). Spatial dynamics were the strongest factor affecting microbial assemblages, with little evidence of temporal dynamics. Spatial dynamics were related to changes in inundation frequency as a result of shore height.

Summary Soil ecosystem functions underpin many ecosystem services. Understanding the drivers of these functions and their stability in response to disturbance is important given land‐use intensification and the predicted increase in disturbance frequency with climate change. Changes in land use and soil abiotic conditions are likely to impact on soil ecosystem functions and their stability, but the effects of changes in soil microbial community structure (i.e. traits, diversity, composition and biomass) are poorly understood. We measured soil abiotic properties, microbial community structure, ecosystem functions (carbon and nutrient cycling) and the stability of functions in response to a dry–rewet cycle, across a land‐use gradient consisting of natural forest, planted forest, high‐ and low‐producing grassland, and vineyards. Results from additive modelling, where explanatory variables were added in a hierarchical manner and retained if significant (land use followed by abiotic variables followed by biotic variables), showed that measures of soil microbial community structure were the only variables able to explain variation in several measures of stability. In contrast, microbial community structure was rarely able to explain further variation in functions measured under static conditions once land use and abiotic factors were accounted for. Consistent with current theory, correlation analysis indicated that fungal : bacterial ratios were negatively related to measures of carbon and nutrient cycling, whereas the Gram‐positive : Gram‐negative ratio was positively related to measures of nutrient cycling and stability. In contrast to current theory, the fungal : bacterial ratio was negatively related to the resistance of soil water‐soluble N contents to drying. Our results show that measures of microbial community structure can be good indicators of a wide range of soil functions and their stability in response to a dry–rewet cycle. Further, they suggest that soil microbial community structure may have a far greater influence on process rates under disturbed, compared to static, conditions. The delivery of ecosystem services in the future may therefore be strongly dependent on the characteristics of the soil microbial community. Lay Summary