Soil Microbial Ecosystem Research Articles

Keystone species affect the relationship between soil microbial diversity and ecosystem function under land use change in subtropical China

AbstractSoil microbial diversity affects soil chemical cycling and ecosystem function. However, how highly connected keystone species regulate associated microbial structure and function (of the whole community and of specialized species), irrespective of their abundance under land use change, remains unresolved.Here, we identified the relationship between microbial diversity [soil phospholipid fatty acid (PLFA) richness and composition, and ammonia‐oxidizing archaea and bacteria (AOA and AOB) communities] with both a broad (i.e. microbial respiration) and specialized function (i.e. nitrification rate) in a woodland, shrubland and adjacent cropland in subtropical China.Microbial respiration was significantly positively related to the microbial richness, but negatively correlated with the keystone species richness across different land use types. The relationships between biodiversity and the broad ecosystem function varied with land use, with a stronger relationship in the afforested land compared with in the cropland. In contrast to the broad function, land use did not significantly affect the specialized function, but the specialized function was positively related to AOA richness in the cropland. Additionally, the specialized function was predominately driven by the keystone species composition in AOA and AOB communities and indirectly regulated by soil environmental factors (particularly soil temperature) across land uses.Overall, our results provide direct experimental insight into the mechanisms underlying the role of the keystone species in regulating below‐ground ecosystem functions under land use change. In particular, our findings reveal that the broad function is maintained by the niche compensation effect, while the specialized function is maintained by the identity effect.A freePlain Language Summarycan be found within the Supporting Information of this article.

Diversity of plant and soil microbes mediates the response of ecosystem multifunctionality to grazing disturbance

Biodiversity drives ecosystem functioning across grassland ecosystems. However, few studies have examined how grazing intensity affects ecosystem multifunctionality (EMF) via its effects on plant diversity and soil microbial diversity in dry grasslands. We conducted a 12-year experiment manipulating sheep grazing intensity in a desert steppe of northern China. Through measuring plant species diversity, soil microbial diversity (bacteria diversity) and multiple ecosystem functions (i.e., aboveground net primary productivity, belowground biomass of plant community, temporal stability of ANPP, soil organic matter, moisture, available nitrogen and phosphorus, ecosystem respiration and gross ecosystem productivity), we aimed to understand how grazing intensity affected EMF via changing the diversity of plants and microbes. Our results showed that increasing grazing intensity significantly reduced EMF and most individual ecosystem functions, as well as the diversity of plants and microbes, while EMF and most individual functions were positively related to plant diversity and soil microbial diversity under all grazing intensities. In particular, soil microbial diversity in shallow soil layers (0–5 cm depth) had stronger positive correlations with plant diversity and EMF than in deeper soil layers. Furthermore, structural equation modeling (SEM) showed that grazing reduced EMF mainly via reducing plant diversity, rather than by reducing soil microbial diversity. Thus, plant diversity played a more important role in mediating the response of EMF to grazing disturbance. This study highlights the critical role of above- and belowground diversity in mediating the response of EMF to grazing intensity, which has important implications for biodiversity conservation and sustainability in arid grasslands.

Bacillus aryabhattai FACU: A promising bacterial strain capable of manipulate the glyphosate herbicide residues.

Glyphosate is a commonly used organophosphate herbicide that has an adverse impact on humans, mammals and soil microbial ecosystems. The redundant utilize of glyphosate to control weed growth cause the pollution of the soil environment by this chemical. The discharge of glyphosate in the agricultural drainage can also cause serious environmental damage and water pollution problems. Therefore, it is important to develop methods for enhancing glyphosate degradation in the soil through bioremediation. In this study, thirty bacterial isolates were selected from an agro-industrial zone located in Sadat City of Monufia Governorate, Egypt. The isolates were able to grow in LB medium supplemented with 7.2 mg/ml glyphosate. Ten isolates only had the ability to grow in a medium containing different concentrations of glyphosate (50, 100, 150, 200 and 250 mg/ml). The FACU3 bacterial isolate showed the highest CFU in the different concentrations of glyphosate. The FACU3 isolate was Gram-positive, spore-forming and rod-shape bacteria. Based on API 50 CHB/E medium kit, biochemical properties and 16S rRNA gene sequencing, the FACU3 isolate was identified as Bacillus aryabhattai. Different bioinformatics tools, including multiple sequence alignment (MSA), basic local alignment search tool (BLAST) and primer alignment, were used to design specific primers for goxB gene amplification and isolation. The goxB gene encodes FAD-dependent glyphosate oxidase enzyme that responsible for biodegradation process. The selected primers were successfully used to amplify the goxB gene from Bacillus aryabhattai FACU3. The results indicated that the Bacillus aryabhattai FACU3 can be utilized in glyphosate-contaminated environments for bioremediation. According to our knowledge, this is the first time to isolate of FAD-dependent glyphosate oxidase (goxB) gene from Bacillus aryabhattai.

Effects of elk and bison carcasses on soil microbial communities and ecosystem functions in Yellowstone, USA

AbstractCarrion is long recognized as important to scavengers. How carrion may affect soil microbial biodiversity and ecosystem processes in natural systems is comparatively unknown, but is important for the intersection of vertebrate food webs, below‐ground processes and ecological heterogeneity.We assessed in situ soil and plant responses to wolf‐killed mammal carrion in Yellowstone National Park, USA.Bison and elk carcasses increased soil respiration and vegetation nutrient concentration and the carcasses contain altered bacterial and fungal communities compared to control plots. The ‘fingerprints’ of soil microbial taxa associated with bison compared to elk carcasses differed considerably and taxa are found dependent upon abiotic gradients and soil properties.We found evidence that soil microbial community changes associated with carcasses may not be as generalizable as previously thought, which is important for a mechanistic understanding of the links between carrion and soil heterogeneity and potentially for applications in forensic science.This work demonstrates the importance of carrion studies in natural systems. Our findings show that carrion creates distinct ecological patterns that contribute to both above‐ and below‐ground biological heterogeneity, linking carrion distribution dynamics with soil microbial biodiversity and ecosystem functions.

Organic mulching positively regulates the soil microbial communities and ecosystem functions in tea plantation

BackgroundDifferent mulches have variable effects on soil physicochemical characteristics, bacterial and fungal communities and ecosystem functions. However, the information about soil microbial diversity, community structure and ecosystem function in tea plantation under different mulching patterns was limited. In this study, we investigated bacterial and fungal communities of tea plantation soils under polyethylene film and peanut hull mulching using high-throughput 16S rRNA and ITS rDNA gene Illumina sequencing.ResultsThe results showed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi, and the dominant fungal phyla were Ascomycota, Mortierellomycota and Basidiomycota in all samples, but different mulching patterns affected the distribution of microbial communities. At the phylum level, the relative abundance of Nitrospirae in peanut hull mulching soils (3.24%) was significantly higher than that in polyethylene film mulching soils (1.21%) in bacterial communities, and the relative abundances of Mortierellomycota and Basidiomycota in peanut hull mulching soils (33.72, 21.93%) was significantly higher than that in polyethylene film mulching soils (14.88, 6.53%) in fungal communities. Peanut hull mulching increased the diversity of fungal communities in 0–20 cm soils and the diversity of bacterial communities in 20–40 cm soils. At the microbial functional level, there was an enrichment of bacterial functional features, including amino acid transport and metabolism and energy production and conversion, and there was an enrichment of fungal functional features, including undefined saprotrophs, plant pathogens and soils aprotrophs.ConclusionsUnique distributions of bacterial and fungal communities were observed in soils under organic mulching. Thus, we believe that the organic mulching has a positive regulatory effect on the soil bacterial and fungal communities and ecosystem functions, and so, is more suitable for tea plantation.

Dibutyl phthalate contamination accelerates the uptake and metabolism of sugars by microbes in black soil

Dibutyl phthalate (DBP) is widely used as plasticizer and has been detected in the environment, posing a threat to animal health. However, the effects of DBP on agricultural microbiomes are not known. In this study, DBP levels in black soil were evaluated, and the impact of DBP contamination on the uptake and metabolism of sugars in microbes was assessed by glucose absorption tests, metaproteomics, metabolomics, enzyme activity assays and computational simulation analysis. The results indicated that DBP contamination accelerated glucose consumption and upregulated the expression of porins and periplasmic monosaccharide ATP-binding cassette (ABC) transporter solute-binding proteins (SBPs). DBP and its metabolic intermediates (carboxymuconate and butanol) may form a stable complex with sugar transporters and enhance the rigidity and stability of these proteins. Sugar metabolism resulting in the generation of ATP and reducing agent (NADPH), as well as the expression of some key enzymes (dehydrogenases) were also upregulated by DBP treatment. Moreover, a diverse bacterial community appears to utilize sugar, suggesting that there are widespread effects of DBP contamination on soil microbial ecosystems. The results of this study provide a theoretical basis for investigating the toxicological effects of DBP on microbes in black soil.

A survey of invasive plants on grassland soil microbial communities and ecosystem services

Invasive plants can cause changes in the structure and function of the ecosystem being invaded. Any changes in ecosystem diversity and community composition will likely alter ecosystem services provided by that ecosystem. However, how these ecosystem services may change is poorly understood. To elucidate how these ecosystem services will change with invasion, we sampled 561 plots undergoing invasion by smooth brome (Bromus inermis) and four other invasive species at a native Rough Fescue prairie located near Saskatoon, Saskatchewan, Canada. Soil and plant surveys were undertaken weekly for 26 weeks between May of 2014 and November of 2014, or the growing season. We measured a suite of ecosystem services, including greenhouse gasses, extracellular enzyme function, forage production, glyphosate degradation and decomposition. Furthermore, soil physical and chemical properties were measured, and soil bacterial and fungal communities were sequenced. This is a large and multifaceted dataset with complex temporal and spatial attributes which can be used to answer numerous questions regarding the functioning of prairie ecosystems and how invasive species will impact that functioning.

Using proxies of microbial community‐weighted means traits to explain the cascading effect of management intensity, soil and plant traits on ecosystem resilience in mountain grasslands

AbstractTrait‐based approaches provide a framework to understand the role of functional biodiversity on ecosystem functioning under global change. While plant traits have been reported as potential drivers of soil microbial community composition and resilience, studies directly assessing microbial traits are scarce, limiting our mechanistic understanding of ecosystem functioning.We used microbial biomass and enzyme stoichiometry, and mass‐specific enzymes activity as proxies of microbial community‐weighted mean (CWM) traits, to infer trade‐offs in microbial strategies of resource use with cascading effects on ecosystem resilience. We simulated a drought event on intact plant–soil mesocosms extracted from mountain grasslands along a management intensity gradient. Ecosystem processes and properties related to nitrogen cycling were quantified before, during and after drought to characterize ecosystem resilience.Soil microbial CWM traits and ecosystem resilience to drought were strongly influenced by grassland type. Structural equation modelling revealed a cascading effect from management to ecosystem resilience through modifications in soil nutrients, and plant and microbial CWM traits. Overall, our results depict a shift from high investment in extracellular enzymes in nutrient‐poor soils (oligotrophic strategy), to a copiotrophic strategy with low microbial biomass N:P and low investment in extracellular enzymes associated with exploitative plant traits in nutrient‐rich soils.Microbial CWM traits responses to management intensity were highly related to ecosystem resilience. Microbial communities with a copiotrophic strategy had lower resistance but higher recovery to drought, while microbial communities with an oligotrophic strategy showed the opposite responses. The unexpected trade‐off between plant and microbial resistance suggested that the lower resistance of copiotrophic microbial communities enabled plant resistance to drought.Synthesis.Grassland management has cascading effects on ecosystem resilience through its combined effects on soil nutrients and plant traits propagating to microbial traits and resilience. We suggest that intensification of permanent grassland management and associated increases in soil nutrient availability decreased plant–microbe competition for N under drought through the selection of drought‐sensitive microbial communities with a copiotrophic strategy that promoted plant resistance. Including proxies of microbial CWM traits into the functional trait framework will strengthen our understanding of soil ecosystem functioning under global change.

Carbon nanomaterials affect carbon cycle-related functions of the soil microbial community and the coupling of nutrient cycles

Many studies have examined changes in soil microbial community structure and composition by carbon nanomaterials (CNMs). Few, however, have investigated their impact on microbial community functions. This study explored how fullerene (C60) and multi-walled carbon nanotubes (M50) altered functionality of an agricultural soil microbial community (Archaea, Bacteria and Eukarya), using microcosm experiments combined with GeoChip microarray. M50 had a stronger effect than C60 on alpha diversity of microbial functional genes; both CNMs increased beta diversity, resulting in functional profiles distinct from the control. M50 exerted a broader, severer impact on microbially mediated nutrient cycles. Together, these two CNMs affected CO2 fixation pathways, microbial degradation of diverse carbohydrates, secondary plant metabolites, lipids and phospholipids, proteins, as well as methanogenesis and methane oxidation. They also suppressed nitrogen fixation, nitrification, dissimilatory nitrogen reduction, eukaryotic assimilatory nitrogen reduction, and anaerobic ammonium oxidation (anammox). Phosphorus and sulfur cycles were less vulnerable; only phytic acid hydrolysis and sulfite reduction were inhibited by M50 but not C60. Network analysis suggested decoupling of nutrient cycles by CNMs, manifesting closer and more hierarchical gene networks. This work reinforces profound impact of CNMs on soil microbial community functions and ecosystem services, laying a path for future investigation in this direction.

Effects of changes in water status on soil microbes and their response mechanism: A review

Soil microbes play essential roles in maintaining terrestrial ecosystem services. Soil moisture is a primary determinant of soil microbial activities and ecosystem functions, which may fluctuate dramatically with the altered precipitation patterns and extreme drought caused by the ongoing global climate change. Due to the distinct soil microbial tolerance and life-strategy approaches to drought stress and different water status, fluctuation of soil moisture has a direct impact on microbial activities and community structure, thereby profoundly affecting microbial-mediated processes and ecosystem functions. Thus, it is of great significance to understand the dynamics and mechanisms that underlie the microbial responses to soil water status. In this review, we summarized recent progress in the study of responses of soil microbial activities (e.g. soil respiration and enzyme activities) and community structure to soil water status. We summarized underlying microbial physiological and ecological mechanisms, particularly 1) the cellular physiological accommodation such as osmolyte accumulation, exopolysaccharide production and transition into dormant states, and 2) the ecological strategies such as stress-resistant gene transfer and functional redundancy. Therefore, this investigation on the underlying relationship between soil microbial assembly and ecosystem functions under different water status could further demonstrate the microbially-mediated soil biogeochemical processes and provide a theoretical basis for future research and modelling of terrestrial ecosystem responses to climate change.

Interactions between biochar and nitrogen impact soil carbon mineralization and the microbial community

Adding biochar (BC) to soils is proposed to enhance carbon sequestration in agricultural soils. However, there is limited knowledge regarding the effects of the interactions between BC and nitrogen (N) on soil organic carbon (SOC) mineralization at an interannual scale. We conducted a three-year field experiment to systematically reveal the impacts of BC combined with N fertilizer on a silty clay soil, including its physicochemical properties, soil respiration characteristics and microbial community. BC applied once at 0, 20 and 40 t ha−1 (B0, B1 and B2, respectively) was combined with three N fertilization levels (0, 120 and 240 kg N ha−1; N0, N1 and N2, respectively). Only winter wheat (Triticum aestivum L.) was cultivated, and it was cultivated in a winter wheat-summer fallow crop system. BC application persistently increased the SOC content by 36.3–91.6% over three years. Several soil parameters were also improved by BC combined with N after one year, such as bulk density, NO3- and available P content. Compared with its values with B0 treatments with N1 or N2, the total soil CO2 emitted decreased by 6.7–8.9% in response to BC combined with N1 but increased by 5.9–7.5% in response to BC combined with N2. B1N1 not only significantly increased microbial biomass but also decreased qCO2. In addition, B1N1 in particular increased the relative abundances of members of the microbial population associated with increased microbial C use efficiency, such as Rhizopus and Helotiaceae. However, B2N1 and B2N2 strongly disturbed the soil microbial ecosystem; moreover, the lowest alpha diversity of the bacterial community was observed in B2N2 soils. In summary, adding BC at a high rate to N-fertilized soil strongly disturbs the soil microbial ecosystem and reduces the C-sequestering potential of soil, while B1N1 treatment is recommended to enhance soil C sequestration and improve soil fertility under dryland farming.

Disturbance Size Can Be Compensated for by Spatial Fragmentation in Soil Microbial Ecosystems

One major interest in soil systems ecology is to maintain ecosystem functions. As soil is exposed to disturbances of different spatial configurations, identifying disturbance characteristics that still allow for maintaining functions is crucial. In macro-ecology, the influence of fragmentation on ecosystems is continuously debated, especially in terms of extinction thresholds on the landscape scale. Whether this influence is positive or negative depends on the considered type of fragmentation: habitat fragmentation often promotes population extinction, whereas spatially fragmented disturbances reduce extinction probability in many cases. In this study, we make use of these concepts to analyze how spatial disturbance characteristics determine functional resilience on the microscale. We used the numerical model eColony considering bacterial growth, substrate consumption and dispersal for analyzing the dynamic response of biodegradation as an exemplary important microbial ecosystem function to disturbance events. We systematically varied the frequency of the disturbance events, and the size and fragmentation of the disturbed area. We found that the influence of the disturbance size on functional recovery depends on the spatial fragmentation of the disturbance, indicating that to some extent disturbance size can be compensated for by the spatial configuration of the disturbed area. In general, biodegradation performance decreases as the disturbed area increases in size and becomes more contiguous. However, if a disturbance is highly fragmented, an increase in disturbance size has no influence on biodegradation performance unless the disturbance is critically large. In this case, the functional performance decreases dramatically. Under recurrent disturbances, this critical disturbance size is shifted towards lower values depending on the disturbance frequency. Our results indicate the importance of spatial disturbance characteristics for functional resilience of soil microbial ecosystems. Critical values for disturbance size and degree of fragmentation emerge from an interplay between both characteristics. Consequently, these characteristics which are widely discussed on the landscape scale need to be equally considered on smaller scales when assessing functional resilience of soil ecosystems.

Reduction in Hg phytoavailability in soil using Hg-volatilizing bacteria and biochar and the response of the native bacterial community.

SummaryBiological approaches are considered promising and eco‐friendly strategies to remediate Hg contamination in soil. This study investigated the potential of two ‘green’ additives, Hg‐volatilizing bacteria (Pseudomonas sp. DC‐B1 and Bacillus sp. DC‐B2) and sawdust biochar, and their combination to reduce Hg(II) phytoavailability in soil and the effect of the additives on the soil bacterial community. The results showed that the Hg(II) contents in soils and lettuce shoots and roots were all reduced with these additives, achieving more declines of 12.3–27.4%, 24.8–57.8% and 2.0–48.6%, respectively, within 56 days of incubation compared to the control with no additive. The combination of DC‐B2 and 4% biochar performed best in reducing Hg(II) contents in lettuce shoots, achieving a decrease of 57.8% compared with the control. Pyrosequencing analysis showed that the overall bacterial community compositions in the soil samples were similar under different treatments, despite the fact that the relative abundance of dominant genera altered with the additives, suggesting a relatively weak impact of the additives on the soil microbial ecosystem. The low relative abundances of Pseudomonas and Bacillus, close to the background levels, at the end of the experiment indicated a small biological disturbance of the local microbial niche by the exogenous bacteria.

Difference in soil bacterial community composition depends on forest type rather than nitrogen and phosphorus additions in tropical montane rainforests

Rapid increase of nitrogen (N) deposition could alter nutrient availability, leading to changes in soil microbial processes and ecosystem carbon and nutrient cycling. However, the effects of N deposition on soil microbes remain elusive in the tropical rainforests in Asia. Here, we conducted a 3-year N addition experiment with four treatments (0, 20, 50, and 100 kg N ha−1 year−1) in a primary and secondary tropical montane forest in Hainan Island, China, to explore the effects of elevated N availability on soil microbial community composition. We also conducted a phosphorus (P) treatment (50 kg P ha−1 year−1) and a N + P treatment (50 kg N ha−1 year−1 + 50 kg P ha−1 year−1) to examine potential P limitation driven by N deposition in highly weathered tropical soils, using a bar-coded pyrosequencing technique. The composition of soil bacterial communities differed dramatically between the primary and secondary forests, but not significant dissimilarity among the fertilization treatments. The community composition, phylogenetic diversity and phylotype richness were significantly correlated with soil pH, total organic C (TOC), and total N (TN), respectively. There were significant differences between the primary and secondary forest in pH, TOC, and TN, but not among the fertilization treatments. These results suggest that differences in soil nutrient status between the primary and secondary forests due to different successional stages rather than chronic N fertilization may be the major factor affecting soil bacterial composition in the tropical montane rainforests.

The microbial network in naturally fertile paddy soil possibly facilitates functional recruitment in the rice mature stage

How agriculture practice, especially the nitrogen fertilization, influences different paddy soil microbial ecosystems remains unclear. The bacterial communities in two paddy fields, which were distinguished by the natural fertility level, were utilized in this study. Each field held two control plots and two nitrogen-fertilized ones. The microbial communities mainly differed in their relative abundances of Proteobacteria and Chloroflexi between the two fields. However, they were very similar in the α-diversity and enzymatic functions, as well as their resistances indexes in response to the nitrogen fertilizers. Redundancy analysis indicated that phosphorus, nitrogen and potassium contents significantly explained the variability of the communities in the two fields total potassium (TK) plus nitrogen level and TK alone significantly explained the variation of the microbial communities in the high yield field and the low yield, respectively. Network analysis data showed that the microbial community in the high-yield field possessed a higher connectivity, which might facilitate recruiting more microbes that were predicted to drive organic matter decomposition, sulfate/iron reduction, nitrogen retention, and methane oxidation at the mature stage. The use of nitrogen fertilizer in the low yield field would help to recruit microbial functions similar to those in the high-yield at the stage. This ecological process possibly stimulated nutrient availability for rice production in the present case.

Forest-to-pasture conversion and recovery based on assessment of microbial communities in Eastern Amazon rainforest.

Amazon rainforest has been subjected to particularly high rates of deforestation caused mainly by the expansion of cattle pasture and agriculture. A commonly observed response to land-use change is a negative impact on biodiversity of plant and animal species. However, its effect on the soil microbial community and ecosystem functioning is still poorly understood. Here, we used a DNA metagenomic sequencing approach to investigate the impact of land-use change on soil microbial community composition and its potential functions in three land-use systems (primary forest, pasture and secondary forest) in the Amazon region. In general, the microbial community structure was influenced by changes in soil physicochemical properties. Aluminum and water-holding capacity significantly correlated to overall community structure and most of microbial phyla. Taxonomic changes were followed by potential functional changes in the soil microbial community, with pasture presenting the most distinct profile in comparison with other sites. Although taxonomic structure was very distinct among sites, we observed a recovery of the potential functions in secondary forest after pasture abandonment. Our findings elucidate a significant shift in belowground microbial taxonomic and potential functional diversity following natural forest re-establishment and have implications for ecological restoration programs in tropical and sub-tropical ecosystems.

Deer and invasive plant removal alters mycorrhizal fungal communities and soil chemistry: Evidence from a long-term field experiment

The invasive plant, garlic mustard (Alliaria petiolata), has the potential to affect soil microbial communities and ecosystem processes in temperate hardwood forests primarily through the release of allelopathic chemicals into the soil. These forest soils are also often affected (directly and indirectly) by the high abundance of white-tailed deer (Odocoileus virginianus), which can alter plant community composition and productivity. We examined the joint effects of deer and garlic mustard on soil microbial communities, soil nutrients and a native plant species’ vital rates in a temperate forest 8 years after initiation of a paired plot deer exclusion/access study where garlic mustard was either removed from half of each plot or remained at ambient level in the other plot half. We examined soil microbial communities using DNA-based techniques and quantified nutrient availability and physicochemical properties. Deer exclusion affected the community structure of AM fungi, particularly when garlic mustard was present, but had no effect on soil chemistry. Garlic mustard removal plots showed no changes for soil fungi, but displayed higher soil carbon content. Interestingly, we found significant changes to native plant vital rates that mirrored soil responses; the presence of garlic mustard led to higher mortality of large, mature plants and reduced native plant cover and biomass. Our data suggest herbivore-plant-soil feedbacks and synergies can interact to negatively affect the soil ecology of forests. Management activities that reduce deer or invasive plant abundance may positively affect soil microbial communities and chemistry in temperate forests.

Grazing-induced microbiome alterations drive soil organic carbon turnover and productivity in meadow steppe

BackgroundGrazing is a major modulator of biodiversity and productivity in grasslands. However, our understanding of grazing-induced changes in below-ground communities, processes, and soil productivity is limited. Here, using a long-term enclosed grazing meadow steppe, we investigated the impacts of grazing on the soil organic carbon (SOC) turnover, the microbial community composition, resistance and activity under seasonal changes, and the microbial contributions to soil productivity.ResultsThe results demonstrated that grazing had significant impacts on soil microbial communities and ecosystem functions in meadow steppe. The highest microbial α-diversity was observed under light grazing intensity, while the highest β-diversity was observed under moderate grazing intensity. Grazing shifted the microbial composition from fungi dominated to bacteria dominated and from slow growing to fast growing, thereby resulting in a shift from fungi-dominated food webs primarily utilizing recalcitrant SOC to bacteria-dominated food webs mainly utilizing labile SOC. Moreover, the higher fungal recalcitrant-SOC-decomposing activities and bacterial labile-SOC-decomposing activities were observed in fungi- and bacteria-dominated communities, respectively. Notably, the robustness of bacterial community and the stability of bacterial activity were associated with α-diversity, while this was not the case for the robustness of fungal community and its associated activities. Finally, we observed that microbial α-diversity rather than SOC turnover rate can predict soil productivity.ConclusionsOur findings indicate the strong influence of grazing on soil microbial community, SOC turnover, and soil productivity and the important positive role of soil microbial α-diversity in steering the functions of meadow steppe ecosystems.

Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France).

Salinity is an important environmental factor influencing microbial community composition. To better understand this influence, we determined the bacterial communities present in 17 different sites of brackish sediment (underwater) and soil (surface) samples from the Camargue region (Rhône river delta) in southern France during the fall of 2013 and 2014 using pyrosequencing of the V3-V4 regions of the 16S rRNA genes amplified by PCR. This region is known for abundant flora and fauna and, though saline, 30% of rice consumed in France is grown here. We found that bacterial abundance in 1g of soil or sediment, calculated by qPCR, was higher in sediments than in surface soil samples. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes phyla dominated the bacterial communities of sediment samples, while members belonging to the Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria, Firmicutes and Acidobacteria phyla dominated the bacterial communities of the soil samples. The most abundant bacterial genera present in the saline sediments and soils from the Camargue belonged mostly to halophilic and sulphate reducing bacteria, suggesting that the Camargue may be a valuable system to investigate saline, yet agriculturally productive, sediment and soil microbial ecosystem.

Small and transient response of winter soil respiration and microbial communities to altered snow depth in a mid-temperate forest

Global climate change is altering snow depth in winter, which could significantly affect soil respiration and microbial communities. However, belowground responses are still uncertain as they depend on the thermal effects on soils, the acclimation of soil microbial communities and ecosystem type. Here, we conducted a snow manipulation experiment including 50% removal of snowpack (mean snow depth after treatment was 3.1 ± 0.7 cm), ambient snow (mean snow depth was 6.3 ± 0.7 cm), and 50% increase of snowpack (mean snow depth after treatment was 9.6 ± 1.5 cm) to explore the effects of altered snow depth on winter soil respiration and microbial communities in a mid-latitude plantation forest with continental climate with dry winters. Winter soil CO2 effluxes varied from 0.09 to 0.84 µmol m−2 s−1 with a mean of 0.32 ± 0.07 µmol m−2 s−1. The cumulative soil CO2 effluxes from 11 December 2014 to 21 March 2015 were 27.3 ± 1.1, 26.5 ± 2.1, and 29.5 ± 1.3 g C m−2 under reduced, ambient and added snowpack, which corresponded to 5.7 ± 0.2%, 5.5 ± 0.3%, and 5.8 ± 0.1% of the annual soil CO2 effluxes, respectively. Our one-year observation results suggested that although snow reduction decreased soil temperature, microbial biomass carbon (MBC) and soil respiration did not change, suggesting microbial adaptation to cold conditions between −4 °C and −1 °C. In contrast, snow addition increased soil temperature, MBC, and soil respiration. Microbial community structure (F/B, ratio of fungi to bacteria) was also changed and soil enzymatic (β-glucosidase) activities increased under snow addition. However, these effects were short-lived and disappeared when soil temperature did not differ between the addition and control plots at the 14th day after treatment. These results indicated that the responses of soil microbial communities and respiratory activities to changing soil temperature were rapid and the response of soil respiration to snow addition was transient. Consequently, altered snow depth did not affect cumulative soil CO2 effluxes. Our study suggests that wintertime soil respiration rates are generally low and snow manipulation has minor effects on soil CO2 efflux, soil temperature (the determinant driver of wintertime soil CO2 efflux) and soil microbial biomass at our site.