Soil Microbial Community Function Research Articles

Soil Bacterial and Fungal Community Responses to Throughfall Reduction in a Eucalyptus Plantation in Southern China

In subtropical plantations in southern China, how soil microbial communities respond to climate change-induced drought is poorly understood. A field experiment was conducted in a subtropical Eucalyptus plantation to determine the impacts of 50% of throughfall reduction (TR) on soil microbial community composition, function, and soil physicochemical properties. Results showed that TR reduced soil water content (SWC) and soil available phosphorus (AP) content. TR significantly altered 196 bacterial operational taxonomic units (OTUs), most of them belonging to Acidobacteria, Actinobacteria, and Proteobacteria, while there were fewer changes in fungal OTUs. At the phylum level, TR increased the relative abundance of Acidobacteria at 0–20 cm soil depth by 37.18%, but failed to influence the relative abundance of the fungal phylum. Notably, TR did not alter the alpha diversity of the bacterial and fungal communities. The redundancy analysis showed that the bacterial communities were significantly correlated with SWC, and fungal communities were significantly correlated with AP content. According to predictions of bacterial and fungal community functions using PICRUSt2 and FUNGuild platforms, TR had different effects on both bacterial and fungal communities. Overall, SWC and AP decreased during TR, resulting in greater changes in soil bacterial community structure, but did not dramatically change soil fungal community structure.

Effects of 2,4-di-tert-butylphenol at different concentrations on soil functionality and microbial community structure in the Lanzhou lily rhizosphere

The autotoxicity of root exudates is an important factor that affects soil enzymes and microbes in rhizosphere soil. Previous studies have confirmed that 2,4-di-tert-butylphenol (2,4-DTBP) is a major autotoxin of the root exudates that severely hampers the yield and quality of Lanzhou lily. However, little is currently known regarding the mechanism of 2,4-DTBP. Here, we hypothesized that 2,4-DTBP has a direct effect on soil functionality and the microbial community structure in Lanzhou lily rhizosphere soil, thereby affecting the growth of Lanzhou lily. To test our hypothesis, various experiments were conducted in this study. We treated Lanzhou lily plants with 2,4-DTBP at different concentrations and analyzed the effects of 2,4-DTBP on rhizosphere soil enzyme activity and microbial community structure and function. The diversity of soil microbes was analyzed using high-throughput sequencing. The results showed that 2,4-DTBP altered rhizosphere soil enzyme activity and microbial community structure and function. Moreover, microbial biomass was stimulated with the addition of 0.5 mM 2,4-DTBP and inhibited with the addition of 2.0 mM 2,4-DTBP. Thus, the 2.0 mM 2,4-DTBP treatment was not suitable for the growth of soil microorganisms. We also found that the 2.0 mM 2,4-DTBP treatment resulted in an increase in the levels of fungal pathogens, such as Fusarium, and reduced the size of beneficial bacterial populations in the rhizosphere soil. Moreover, the effects of 2,4-DTBP on soil functionality and the microbial community structure differed based on the concentrations of 2,4-DTBP and the specific indexes of determination. Thus, we concluded that 2,4-DTBP could inhibit soil functionality and disturb the microbial community structure in the rhizosphere soil. This finding may be important for understanding the relationship between autotoxicity and barriers and clarifying the long-term continuous cropping problems of Lanzhou lily.

Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland.

Microbial communities are early responders to wetland degradation, and instrumental players in the reversal of this degradation. However, our understanding of soil microbial community structure and function throughout wetland development remains incomplete. We conducted a survey across cranberry farms, young retired farms, old retired farms, flooded former farms, ecologically restored former farms, and natural reference wetlands with no history of cranberry farming. We investigated the relationship between the microbial community and soil characteristics that restoration intends to maximize, such as soil organic matter, cation exchange capacity and denitrification potential. Among the five treatments considered, flooded and restored sites had the highest prokaryote and microeukaryote community similarity to natural wetlands. In contrast, young retired sites had similar communities to farms, and old retired sites failed to develop wetland microbial communities or functions. Canonical analysis of principal coordinates revealed that soil variables, in particular potassium base saturation, sodium, and denitrification potential, explained 45% of the variation in prokaryote communities and 44% of the variation in microeukaryote communities, segregating soil samples into two clouds in ordination space: farm, old retired and young retired sites on one side and restored, flooded, and natural sites on the other. Heat trees revealed possible prokaryotic (Gemmatimonadetes) and microeukaryotic (Rhizaria) indicators of wetland development, along with a drop in the dominance of Nucletmycea in restored sites, a class that includes suspected mycorrhizal symbionts of the cranberry crop. Flooded sites showed the strongest evidence of wetland development, with triple the soil organic matter accumulation, double the cation exchange capacity, and seventy times the denitrification potential compared to farms. However, given that flooding does not promote any of the watershed or habitat benefits as ecological restoration, we suggest that flooding can be used to stimulate beneficial microbial communities and soil functions during the restoration waiting period, or when restoration is not an option.

The nitrification inhibitor nitrapyrin has non-target effects on the soil microbial community structure, composition, and functions

Nitrapyrin is a nitrification inhibitor used to retain ammonia-N in soil to improve crop yields and quality. Nitrapyrin targets specifically the ammonia oxidizers, but it is not known if it has non-target effects on the soil microbial communities. Here, we tested the hypothesis that nitrapyrin also leads to large shifts in soil microbial community structure, composition, diversity and functions. To test this hypothesis, we set-up a field experiment where wheat (Triticum aestivum cv. AC Walton) was fertilized with ammonium nitrate (NH4NO3) and supplemented or not with nitrapyrin. Rhizosphere and bulk soils were sampled twice (at grain filling and harvest), the 16S rRNA gene and ITS region were amplified and sequenced to follow the changes in archaeal, bacterial and fungal community structure, composition and diversity. To assess microbial functions, several genes involved in the nitrogen cycle were quantified by real-time qPCR, and volatile organic compounds (VOCs) were trapped in the rhizosphere at the moment of sampling. Sampling dates and soil compartments had overwhelming effects on the microbial communities. However, nitrapyrin still significantly affected the relative abundance of Thaumarchaeota, Proteobacteria, Nitrospirae and Basidiomycota, and several genera. Nitrapyrin also significantly affected bacterial and fungal community structure, and the abundance of all the N-cycle gene tested, but always in interaction with the sampling date. In contrast, nitrapyrin had no significant effect on the emission of VOCs, where only sampling dates significantly influenced the profiles observed. Our results show that nitrapyrin influences non-target soil- and plant-associated microbial communities. In the longer term, these shifts might counteract the positive effect of nitrapyrin on crop nutrition and greenhouse gas emissions.

Fluoroalkylether compounds affect microbial community structures and abundance of nitrogen cycle-related genes in soil-microbe-plant systems

As alternatives to conventional PFAS, ether-PFAS have not been studied much. Their effects to microbial communities, in particular, have not been reported. In this study, we investigated change of microbial community in soil-plant systems dosed with undecafluoro-2-methyl-3-oxahexanoic acid (GenX), dodecafluoro-3H-4,8-dioxanonanoate (ADONA), or 9-chlorohexadecafluoro-3-oxanonane-1-sulfonate (F-53B). It is revealed that the community structure and the species diversity were significantly affected by each of the three ether-PFAS at the two tested concentrations. The only exception was GenX at the low concentration. With respect to nitrification, amoA genes in ammonia oxidizing bacteria were not significantly affected while amoA gene abundance in ammonia oxidizing archaea was significantly decreased. In terms of denitrification, ether-PFAS at different concentrations had different impacts to the three studied genes: nirS, nirK, and norZ. This study thus demonstrated that ether-PFAS could bring significant changes to the soil microbial community structure and functions.

Elevated CO2 affects the rhizosphere microbial community and the growth of two invader plant species differently in semiarid Mediterranean soils

AbstractThe rise in atmospheric CO2 levels is foreseen to enhance the growth of exotic invasive plants and potentially alter the rhizosphere microbial community, which in turn could enhance the risk of colonization by such invaders. This response could be determined by the plant type and the features of invaded soil. The goal of this investigation was to compare the effects of elevated CO2 on the rhizosphere bacterial and fungal communities of two invaders with distinct degrees of invasiveness, Nicotiana glauca and Mirabilis jalapa, by growing the plants in five different semiarid soils at ambient (410 ppm) or elevated (760 ppm) CO2. The changes in soil physicochemical, biochemical, and biological features mediated by the invaders were also evaluated. The effect of CO2 supply on shoot dry biomass was only significant for N. glauca, the shoot and root biomass of plants grown under elevated CO2 being approximately 53% and 14% greater, respectively, than those of the plants grown under ambient CO2. Elevated CO2 only promoted shifts in the rhizosphere bacterial community composition and enhanced the bacterial functional potential related to nucleoside and nucleotide biosynthesis and N‐cycling in N. glauca. Among the bacterial indicator species, the genera Sphingomonas, Stenotrophobacter, and Gaiella were more abundant in the rhizosphere of N. glauca plants grown under elevated CO2. This study demonstrates that the responses of aboveground and belowground biomass of invasive plants to CO2 enrichment, as well as those of the composition and functioning of soil microbial communities, are dependent on their degree of invasiveness.

Silver nanomaterials released from commercial textiles have minimal impacts on soil microbial communities at environmentally relevant concentrations

Silver nanomaterials (Ag NMs) have been used in a variety of commercial products to take advantage of their antimicrobial properties. However, there are concerns that these AgNMs can be released during/after use and enter wastewater streams, potentially impacting aquatic systems or accumulating in wastewater biosolids. Biosolids, which are a residual of wastewater treatment processes, have been found to contain AgNMs and are frequently used as agricultural fertilizer. Since the function of soil microbial communities is imperative to nutrient cycling and agricultural productivity, it is important to characterize and assess the effects that silver nanomaterials could have in agricultural soils. In this study agricultural soil was amended with pristine engineered (PVP-coated or uncoated AgNMs), aged silver (sulphidized or released from textiles) nanomaterials, and ionic silver to determine the fate and toxicity over the course of three months. Exposures were carried out at various environmentally relevant concentrations (1 and 10 mg Ag/kg soil) representing between 30 to over 800 years of equivalent biosolid loadings. Over thirteen different methodologies and measures were used throughout this study to assess for potential effects of the silver nanomaterials on soil, including microbial community composition, average well colour development (AWCD) and enzymatic activity. Overall, the AgNM exposures did not exhibit significant toxic effects to the soil microbial communities in terms of density, activity, function and diversity. However, the positive ionic silver treatment (100 mg Ag/kg soil) resulted in suppression to microbial activity while also resulting in significantly higher populations of Frankia alni (nitrogen-fixer) and Arenimonas malthae (phytopathogen) as compared to the negative control (p < 0.05, Tukey HSD) which warrants further investigation.

The influence of alfalfa-switchgrass intercropping on microbial community structure and function.

The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N2 O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N2 O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.

Scale dependence in functional equivalence and difference in the soil microbiome

Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (Quercus rubra L.) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. A similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Notably, for the site with pronounced local-scale functional legacies, there was much greater within-site variation in field-soil microsite moisture than at the site which did not exhibit functional legacies, suggesting that the extent of local-scale variation in microclimate may act as control on whether local-scale functional legacies are observed. Regardless of whether this mechanism does explain our findings, our observations do confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extend this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes are associated with microbial functional legacies.

Changes in soil bacterial and fungal communities in response to Bacillus megaterium NCT-2 inoculation in secondary salinized soil.

BackgroundSecondary salinized soil in greenhouses often contains excess nitrate. Inoculation of Bacillus megaterium NCT-2 with nitrate assimilation ability represents an attractive approach for soil remediation. However, the effects of NCT-2 on the structure and function of soil microbial communities have not been explored.MethodsGreenhouse experiments were carried out to investigate changes in soil properties, Brassica chinensis L. growth, bacterial, and fungal community structure and function in response to NCT-2 inoculation.ResultsThe NCT-2 inoculant significantly reduced the nitrate content in B. chinensis and inhibited the rebound of soil nitrate in the later stage. The shifts of bacterial community structure and function by NCT-2 was negligible, and a greater disturbance of soil fungal community structure and function was observed, for example the strong inhibitory effect on ectomycorrhizal fungi. These results indicated that the NCT-2 inoculant likely achieved the remediation effect in secondary salinized soil by shifting fungal community. The present findings add to the current understanding of microbial interactions in response to bacterial inoculation and can be of great significance for the application of NCT-2 inoculants in secondary salinized soil remediation.

Biodegradable and conventional microplastics exhibit distinct microbiome, functionality, and metabolome changes in soil

Environmental concerns with liberal petroleum-based plastic use have led to demand for sustainable biodegradable alternatives. However, the inadequate end-of-life treatment of plastics may emit microplastics, either conventional or biodegradable, to the terrestrial environment. It is essential to evaluate the possible effects of conventional and biodegradable microplastics on the composition and function of soil microbial communities. Therefore, we conducted a soil microcosm experiment with polyethylene (PE), polystyrene (PS), polylactide (PLA), or polybutylene succinate (PBS) microplastics. The soil microbiome and metabolome were evaluated via 16S rRNA gene sequencing, metagenomics, and untargeted metabolomics. We reported that the presence of conventional or biodegradable microplastics can significantly alter soil microbial community composition. Compared to the control soils, the microbiome in PBS and PLA amended soils exhibited higher potential for uptake of exogenous carbohydrates and amino acids, but a reduced capacity for related metabolic function, potentially due to catabolite repression. No differences in soil metabolome can be observed between conventional microplastic treatments and the control. The potential reason may be that the functional diversity was unaffected by PE and PS microplastics, while the biodegradable particles promoted the soil microbial multifunctionality. Our findings systematically shed light on the influence of conventional and biodegradable microplastics on soil microorganisms, facilitating microplastic regulation.

Understanding Responses of Soil Microbiome to the Nitrogen and Phosphorus Addition in Metasequoia glyptostroboides Plantations of Different Ages.

Nitrogen (N) and phosphorus (P) have significant effects on soil microbial community diversity, composition, and function. Also, trees of different life stages have different fertilization requirements. In this study, we designed three N additions and three P levels (5years of experimental treatment) at two Metasequoia glyptostroboides plantations of different ages (young, 6years old; middle mature, 24years old) to understand how different addition levels of N and P affect the soil microbiome. Here, the N fertilization of M. glyptostroboides plantation land (5years of experimental treatment) significantly enriched microbes (e.g., Lysobacter, Luteimonas, and Rhodanobacter) involved in nitrification, denitrification, and P-starvation response regulation, which might further lead to the decreasing in alpha diversity (especially in 6YMP soil). The P addition could impact the genes involved in inorganic P-solubilization and organic P-mineralization by increasing soil AP and TP. Moreover, the functional differences in the soil microbiomes were identified between the 6YMP and 24YMP soil. This study provides valuable information that improves our understanding on the effects of N and P input on the belowground soil microbial community and functional characteristics in plantations of different stand ages.

Microbial investigations of new hydrogel-biochar composites as soil amendments for simultaneous nitrogen-use improvement and heavy metal immobilization

Agricultural sustainability is challenging because of increasingly serious and co-existing issues, e.g., poor nitrogen-fertilizer use and heavy metal pollution. Herein, we introduced a new poly(acrylic acid)-grafted chitosan and biochar composite (PAA/CTS/BC) for soil amendment, and provided a first microbial insight into how PAA/CTS/BC amendment simultaneously improved nitrogen cycling and immobilized heavy metals. Our results suggest that the PAA/CTS/BC amendment significantly promoted soil ammonium retention, and reduced nitrate accumulation, nitrous oxide emission and ammonia volatilization during the rice cultivation. The availability of various heavy metals (Fe, Mn, Cu, Zn, Ni, Pb, Cr, and As) markedly decreased in the PAA/CTS/BC amended soil, thereby reducing their accumulation in rice root. The PAA/CTS/BC amendment significantly altered the structure and function of soil microbial communities. Importantly, the co-occurrence networks of microbial communities became more complex and function-specific after PAA/CTS/BC addition. For example, the keystone species related to organic matter degradation, denitrification, and plant resistance to pathogen or stresses were enriched within the network. In addition to direct adsorption, the effects of PAA/CTS/BC on shaping microbial communities played dominant roles in the soil amendment. Our findings provide a promising strategy of simultaneous nitrogen-use improvement and heavy metal immobilization for achieving crop production improvement, pollution control, and climate change mitigation.

Microbial Substrate Utilization and Vegetation Shifts in Boreal Forest Floors of Western Canada

Boreal forest soils are highly susceptible to global warming, and in the next few decades, are expected to face large increases in temperature and transformative vegetation shifts. The entire boreal biome will migrate northward, and within the main boreal forest of Western Canada, deciduous trees will replace conifers. The main objective of our research was to assess how these vegetation shifts will affect functioning of soil microbial communities and ultimately the overall persistence of boreal soil carbon. In this study, aspen and spruce forest floors from the boreal mixedwood forest of Alberta were incubated in the laboratory for 67 days without (control) and with the addition of three distinct 13C labeled substrates (glucose, aspen leaves, and aspen roots). Our first objective was to compare aspen and spruce substrate utilization efficiency (SUE) in the case of a labile C source (13C-glucose). For our second objective, addition of aspen litter to spruce forest floor mimicked future vegetation shifts, and we tested how this would alter substrate use efficiency in the spruce forest floor compared to the aspen. Tracking of carbon utilization by microbial communities was accomplished using 13C-PLFA analysis, and 13C-CO2 measurements allowed quantification of the relative contribution of each added substrate to microbial respiration. Following glucose addition, the aspen community showed a greater 13C-PLFA enrichment than the spruce throughout the 67-day incubation. The spruce community respired a greater amount of 13C glucose, and it also had a much lower glucose utilization efficiency compared to the aspen. Following addition of aspen litter, in particular aspen leaves, the aspen community originally showed greater total 13C-PLFA enrichment, although gram positive phospholipid fatty acids (PLFAs) were significantly more enriched in the spruce community. While the spruce community respired a greater amount of the added 13C-leaves, both forest floor types showed comparable substrate utilization efficiencies by Day 67. These results indicate that a shift from spruce to aspen may lead to a greater loss of the aspen litter through microbial respiration, but that incorporation into microbial biomass and eventually into the more persistent soil carbon pool may not be affected.

Microbial community responses to multiple soil disinfestation change drivers

Soil continuous cropping obstacles lead to yield and economic losses in agriculture. Reductive soil disinfestation (RSD) is an effective technology for alleviating it. However, the key factors influencing microbial community composition and how do they promote functional transformation of core microbes under RSD practice remain poorly understood. Hence, a short-term field experiment was performed integrating real-time polymerase chain reaction, average well color development (AWCD), and MiSeq pyrosequencing to investigate relationships between environmental factors and microorganisms in five different disinfestation treatments, i.e., untreated monoculture soil (CK), soil with high temperature heating (HT), soil with dazomet (DZ), RSD with sugarcane bagasse (SB), or with bean dregs (BD). The results showed that compared to non-RSD treatments, both RSD treatments significantly increased soil microbial abundance and soil available K and organic matter (OM). Further analysis found that available K and OM were the key factors inducing microbial community change. Additionally, relative to non-RSD treatments, the relative abundances of phyla Proteobacteria, Acidobacteria, Rokubacteria, and Ascomycota were higher, whereas those of Actinobacteria, Gemmatimonadetes, and Basidiomycota were lower in RSD treatments. Changes in microbial diversity and abundance led to variation of soil microbial community functions. AWCD and community function prediction showed that, in contrast with non-RSD treatments, soil metabolism activity significantly increased, bacterial community functions including terpenoids and polyketides metabolism, signal transduction and cell motility increased, and the number of saprotroph fungi increased under RSD treatments. Overall, RSD incorporated with sugarcane bagasse or bean dregs efficiently improved soil fertility, and considerably increased soil microbial activity and function, which may benefit future sustainable agriculture production. Key points • Reductive soil disinfestation can alleviate continuous cropping obstacles by improving soil fertility. • Organic matter and available potassium as the key factors affected microbial community reconstruction and function. • Reductive soil disinfestation can improve soil metabolic activity and functional diversity by altering microorganism community.

Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China.

Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.

Seasonality regulates the effects of acid rain on microbial community in a subtropical agricultural soil of Southern China

Acid rain alters soil carbon (C) cycling by influencing the soil microbial community structure and functions. However, the response of soil microbial communities to acid rain with time and underlying mechanisms are still poorly understood. Herein, we conducted a one-year intact soil core experiment to investigate the temporal changes of soil microbial community composition and C sources metabolism under acid rain (pH 5.0, pH 4.0, and pH 3.0) in an agricultural soil of southern China. We found that pH 3.0 acid rain increased the total, bacterial, gram-positive bacterial, and actinomycetal PLFAs at the early stage, but this effect diminished with time. Conversely, the gram-negative bacterial PLFAs contents were reduced under pH 3.0 acid rain at the later stage. Interestingly, pH 5.0 acid rain increased the total, bacterial, gram-positive bacterial, and actinomycetal PLFAs contents at the later stage. In addition, pH 3.0 and pH 5.0 acid rain treatments accordingly altered the soil microbial community structure at the early and later stage. However, acid rain did not change the microbial C sources utilization pattern. The principal response curve analysis revealed that the seasonal variation exerted a greater effect on the overall variance of soil microbial community structure than the acidity of acid rain. Our results demonstrate the asynchronous response of soil microbial community structure and function, which implies that the microbial functional redundancy may exist in the subtropical agricultural soil under acid rain.

Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning

Microbial respiration is critical for soil carbon balance and ecosystem functioning. Previous studies suggest that plant diversity influences soil microbial communities and their respiration. Yet, the linkages between tree diversity, microbial biomass, microbial diversity, and microbial functioning have rarely been explored. In this study, we measured two microbial functions (microbial physiological potential, and microbial respiration), together with microbial biomass, microbial taxonomic and functional profiles, and soil chemical properties in a tree diversity experiment in South China, to disentangle how tree diversity affects microbial respiration through the modifications of the microbial community. Our analyses show a significant positive effect of tree diversity on microbial biomass (+25% from monocultures to 24-species plots), bacterial diversity (+12%), and physiological potential (+12%). In addition, microbial biomass and physiological potential, but not microbial diversity, were identified as the key drivers of microbial respiration. Although soil chemical properties strongly modulated soil microbial community, tree diversity increased soil microbial respiration by increasing microbial biomass rather than changing microbial taxonomic or functional diversity. Overall, our findings suggest a prevalence of microbial biomass over diversity in controlling soil carbon dynamics.

Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils.

ABSTRACTComputational approaches that link bacterial 16S rRNA gene amplicon data to functional genes based on prokaryotic reference genomes have emerged. This study aims to validate or refute the applicability of the functional gene prediction tools for assessment and comparison of community functionality among experimental treatments, inducing either fast or slow responses in rhizosphere microbial community composition and function. Rhizosphere samples of wheat and barley were collected in two consecutive years at active and mature growth phases from organic and conventional farming plots with ambient or future-climate treatments of the Global Change Experimental Facility. Bacterial community composition was determined by 16S rRNA gene amplicon sequencing, and the activities of five extracellular enzymes involved in carbon (β-glucosidases, cellobiohydrolase, and xylosidase), nitrogen (N-acetylglucosaminidase), and phosphorus (acid phosphatase) cycles were determined. Structural community data were used to predict functional patterns of the rhizosphere communities using Tax4Fun and PanFP. Subsequently, the predictions were compared with the measured activities. Despite the fact that different treatments mainly drove either community composition (plant growth phase) or measured enzyme activities (farming system), the predictions mirrored patterns in the treatments in a qualitative but not quantitative way. Most of the discrepancies between measured and predicted values resulted from plant growth stages (fast community response), followed by farming management and climate (slower community response). Thus, our results suggest the applicability of the prediction tools for comparative investigations of soil community functionality in less-dynamic environmental systems.IMPORTANCE Linking soil microbial community structure to its functionality, which is important for maintaining health and services of an ecosystem, is still challenging. Besides great advances in structural community analysis, functional equivalents, such as metagenomics and metatranscriptomics, are still time and cost intensive. Recent computational approaches (Tax4Fun and PanFP) aim to predict functions from structural community data based on reference genomes. Although the usability of these tools has been confirmed with metagenomic data, a comparison between predicted and measured functions is so far missing. Thus, this study comprises an expansive reality test on the performance of these tools under different environmental conditions, including relevant global change factors (land use and climate). The work provides a valuable validation of the applicability of the prediction tools for comparison of soil community functions across different sufficiently established soil ecosystems and suggest their usability to unravel the broad spectrum of functions provided by a given community structure.

Effects of conservation tillage on soil microbial community and the function of soil carbon cycling

Agricultural tillage practices significantly affect the structure and function of soil micro-bial community, as well as its control over soil carbon cycling. Conservation tillage practice based on no-tillage and crop straw returning is an important measure to improve soil carbon sequestration and fertility, in which soil microorganisms play a key role. Although many previous studies focus on the structure and function of microbial communities under conservation tillage, our overall understanding of soil microbial responses at community level upon conservation tillage is still lacking, due to the complexity of the soil, environmental factors and the different selections of microbial research methods. Furthermore, previous studies paid more attention to the role of soil microorganisms as decomposers and the contribution of plant-derived carbon to the formation of soil carbon pool, but ignored the contribution of microbial-derived carbon to the formation and stability of soil carbon pool. We summarized the paradigm shift in soil organic matter formation and stability theories, reviewed the research methods of soil microbial community, focused on the effects of conservation tillage on soil microbial biomass, community diversity and composition, carbon metabolism, as well as microbial-derived carbon storage, and proposed suggestions for future study, aiming to provide support for future studies regarding microbial responses and its control over soil carbon dynamics in agroecosystem.