Atmospheric N Deposition Increases Bacterial Laccase-Like Multicopper Oxidases: Implications for Organic Matter Decay

Anthropogenic release of biologically available nitrogen (N) has increased dramatically over the last 150 years, which can alter the processes controlling carbon (C) storage in terrestrial ecosystems. In a northern hardwood forest ecosystem located in Michigan in the United States, nearly 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This change occurred concomitantly with compositional changes in Basidiomycete fungi and in Actinobacteria, as well as the downregulation of fungal lignocelluloytic genes. Recently, laccase-like multicopper oxidases (LMCOs) have been discovered among bacteria which can oxidize β-O-4 linkages in phenolic compounds (e.g., lignin and humic compounds), resulting in the production of dissolved organic carbon (DOC). Here, we examined how nearly 2 decades of experimental N deposition has affected the abundance and composition of saprotrophic bacteria possessing LMCO genes. In our experiment, LMCO genes were more abundant in the forest floor under experimental N deposition whereas the abundances of bacteria and fungi were unchanged. Experimental N deposition also led to less-diverse, significantly altered bacterial and LMCO gene assemblages, with taxa implicated in organic matter decay (i.e., Actinobacteria, Proteobacteria) accounting for the majority of compositional changes. These results suggest that experimental N deposition favors bacteria in the forest floor that harbor the LMCO gene and represents a plausible mechanism by which anthropogenic N deposition has reduced decomposition, increased soil C storage, and accelerated phenolic DOC production in our field experiment. Our observations suggest that future rates of atmospheric N deposition could fundamentally alter the physiological potential of soil microbial communities.     

Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots

Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (?31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin‐derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin‐derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin‐derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.     

Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition

Future rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems.     

Anthropogenic N deposition increases soil organic matter accumulation without altering its biochemical composition

Accumulating evidence indicates that future rates of atmospheric N deposition have the potential to increase soil C storage by reducing the decay of plant litter and soil organic matter (SOM). Although the microbial mechanism underlying this response is not well understood, a decline in decay could alter the amount, as well as biochemical composition of SOM. Here, we used size‐density fractionation and solid‐state ¹³C‐NMR spectroscopy to explore the extent to which declines in microbial decay in a long‐term (ca. 20 yrs.) N deposition experiment have altered the biochemical composition of forest floor, bulk mineral soil, as well as free and occluded particulate organic matter. Significant amounts of organic matter have accumulated in occluded particulate organic matter (~20%; oPOM); however, experimental N deposition had not altered the abundance of carboxyl, aryl, alkyl, or O/N‐alkyl C in forest floor, bulk mineral soil, or any soil fraction. These observations suggest that biochemically equivalent organic matter has accumulated in oPOM at a greater rate under experimental N deposition, relative to the ambient treatment. Although we do not understand the process by which experimental N deposition has fostered the occlusion of organic matter by mineral soil particles, our results highlight the importance of interactions among the products of microbial decay and the chemical and physical properties of silt and clay particles that occlude organic matter from microbial attack. Because oPOM can reside in soils for decades to centuries, organic matter accumulating under future rates of anthropogenic N deposition could remain in soil for long periods of time. If temperate forest soils in the Northern Hemisphere respond like those in our experiment, then unabated deposition of anthropogenic N from the atmosphere has the potential to foster greater soil C storage, especially in fine‐texture forest soils.     

Investigating microbial associations from sequencing survey data with co‐correspondence analysis

Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next‐generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co‐correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co‐occurrence networks and thus investigate the presence of patterns in ecological networks.     

Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition

The fungal community of the forest floor was examined as the cause of previously reported increases in soil organic matter due to experimental N deposition in ecosystems producing predominantly high-lignin litter, and the opposite response in ecosystems producing low-lignin litter. The mechanism proposed to explain this phenomenon was that white-rot basidiomycetes are more important in the degradation of high-lignin litter than of low-lignin litter, and that their activity is suppressed by N deposition. We found that forest floor mass in the low-lignin sugar-maple dominated system decreased in October due to experimental N deposition, whereas forest floor mass of high-lignin oak-dominated ecosystems was unaffected by N deposition. Increased relative abundance of basidiomycetes in high-lignin forest floor was confirmed by denaturing gradient gel electrophoresis (DGGE) and sequencing. Abundance of basidiomycete laccase genes, encoding an enzyme used by white-rot basidiomycetes in the degradation of lignin, was 5-10 times greater in high-lignin forest floor than in low-lignin forest floor. While the differences between the fungal communities in different ecosystems were consistent with the proposed mechanism, no significant effects of N deposition were detected on DGGE profiles, laccase gene abundance, laccase length heterogeneity profiles, or phenol oxidase activity. Our observations indicate that the previously detected accumulation of soil organic matter in the high-lignin system may be driven by effects of N deposition on organisms in the mineral soil, rather than on organisms residing in the forest floor. However, studies of in situ gene expression and temporal and spatial variability within forest floor communities will be necessary to further relate the ecosystem dynamics of organic carbon to microbial communities and atmospheric N deposition.     

Anthropogenic modification disrupts species co‐occurrence in stream invertebrates

The question of whether species co‐occurrence is random or deterministic has received considerable attention, but little is known about how anthropogenic disturbance mediates the outcomes. By combining experiments, field surveys and analysis against null models, we tested the hypothesis that anthropogenic habitat modification disrupts species co‐occurrence in stream invertebrates across spatial scales. Whereas communities in unmodified conditions were structured deterministically with significant species segregation, catchment‐scale conversion to agriculture and sediment deposition at the patch‐ or micro‐habitat scale apparently randomized species co‐occurrences. This shift from non‐random to random was mostly independent of species richness, abundance and spatial scale. Data on community‐wide life‐history traits (body size, dispersal ability and predatory habits) and beta‐diversity indicated that anthropogenic modification disrupted community assembly by affecting biotic interactions and, to a lesser extent, altering habitat heterogeneity. These data illustrate that the balance between predictable and stochastic patterns in communities can reflect anthropogenic modifications that not only transcend scales but also change the relative forces that determine species coexistence. Research into the effects of habitat modification as a key to understanding global change should extend beyond species richness and composition to include species co‐occurrence, species interactions and any functional consequences.     

Ant mosaics occur in SE Asian oil palm plantation but not rain forest and are influenced by the presence of nest‐sites and non‐native species

Interaction networks within biotic communities can be dramatically altered by anthropogenic habitat modification. Ants, an important ecological group, often interact competitively to form mosaic‐like patterns in disturbed plantation habitats, in which dominant species form mutually exclusive territories. However, the existence of these ant mosaics in pristine forests is contentious. Here we assess the relative strengths of ant competitive interactions in oil palm plantation and primary rain forest in Sabah, Malaysia, using null models of species co‐occurrence. We use two metrics: the C‐score, which measures mean degree of overall co‐occurrence, and a novel metric, the C_var‐score, which measures the variance in degree of co‐occurrence. We also investigate the role of nest sites by collecting ants from canopy and leaf litter microhabitats, and from epiphytic ferns, an important nest site for canopy ants. Furthermore, we assess whether non‐native species, which were widespread in oil palm plantation (61 occurrences vs five in rain forest) are important in driving the formation of ant mosaics. We found no evidence for ant mosaics in any primary forest microhabitat. In oil palm plantation, segregation between species was pronounced in epiphytes, weak in the rest of the canopy and absent in leaf litter communities. Intriguingly, exclusion of non‐native ant species from analyses increased the degree of negative species co‐occurrence in all three microhabitats, with species segregation in the oil palm canopy becoming statistically significant. Our results suggest that invasion of plantation habitats by non‐native species does not drive increased species segregation in ant communities. Rather, high degrees of species segregation might relate to changes in the importance of canopy nest sites, with colonies competing more strongly for these in plantations. In primary forests, weaker nest‐site limitation and the highly complex, more vertically stratified, non‐uniform canopy could lead to random co‐occurrence between ant species at the scales studied here.     

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, “omics” approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.     

Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.Subject terms: Soil microbiology, Ecology     

Geospatial variation in co‐occurrence networks of nitrifying microbial guilds

Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.     

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.     

Tree Species Richness Strengthens Relationships between Ants and the Functional Composition of Spider Assemblages in a Highly Diverse Forest

In species‐rich ecosystems, such as subtropical and tropical forests, higher trophic level interactions are key mediators of ecosystem functioning. Plant species loss may alter these interactions, but the effects of plant diversity might be modified by intraguild interactions, particularly among predators. We analyzed the relationships between spiders and ants, two dominant predatory arthropod taxa, on tree saplings across a gradient from medium to high woody plant species richness in a subtropical forest in Southeast China. Neither ant nor spider total biomass was significantly related to plant species richness. By contrast, the biomass distribution of web‐building and hunting spiders changed and spider family richness increased in the presence of ants, resulting in more web builder‐dominated assemblages. However, these relationships depended on the plant communities, and were stronger in plots with higher plant species richness. Our results indicate that in addition to potential effects of ants on hunting spiders in particular, ants could indirectly influence intraguild interactions within spider assemblages. The observed shifts in the spider assemblages with increasing ant presence and plant species richness may have functional consequences, as web‐building and hunting spiders have distinct prey spectra. The relationships among ants, spiders, and plant species richness might contribute to explaining the non‐significant relationship between the overall effects of predators and plant diversity previously observed in the same forest plots. Our findings thus give insight into the complexity of biotic interactions in such species‐rich ecosystems.     

Direct effects of temperature on forest nitrogen cycling revealed through analysis of long‐term watershed records

The microbial conversion of organic nitrogen (N) to plant available forms is a critical determinant of plant growth and carbon sequestration in forests worldwide. In temperate zones, microbial activity is coupled to variations in temperature, yet at the ecosystem level, microbial N mineralization seems to play a minor role in determining patterns of N loss. Rather, N losses often appear to vary with seasonality in hydrology and plant demand, while exports over longer periods are thought to be associated with increasing rates of anthropogenic N deposition. We analyzed long‐term (21–32 years) time series of climate and stream and atmospheric chemistry from two temperate deciduous forest watersheds in the southeastern USA to understand the sensitivity of internal forest N cycles to climate variation and atmospheric deposition. We evaluated the time series with a simple analytical model that incorporates key biotic constraints and mechanisms of N limitation and cycling in plant–soil systems. Through maximum likelihood analysis, we derive biologically realistic estimates of N mineralization and its temperature sensitivity (Q₁₀). We find that seasonality and long‐term trends in stream nitrate (NO₃) concentrations can in large part be explained by the dynamics of internal biological cycling responding to climate rather than external forcing from atmospheric chemistry. In particular, our model analysis suggests that much of the variation in N cycling in these forests results from the response of microbial activity to temperature, causing NO₃ losses to peak in the growing season and to accelerate with recent warming. Extrapolation of current trends in temperature and N deposition suggests that the upturn in temperature may increase future N export by greater than threefold more than from increasing deposition, revealing a potential direct effect of anthropogenic warming on terrestrial N cycles.     

Cyanobacteria drive community composition and functionality in rock–soil interface communities

Most ecological research on hypoliths, significant primary producers in hyperarid deserts, has focused on the diversity of individual groups of microbes (i.e. bacteria). However, microbial communities are inherently complex, and the interactions between cyanobacteria, heterotrophic bacteria, protista and metazoa are likely to be very important for ecosystem functioning. Cyanobacterial and heterotrophic bacterial communities were analysed by pyrosequencing, while metazoan and protistan communities were assessed by T‐RFLP analysis. Microbial functionality was estimated using carbon substrate utilization. Cyanobacterial community composition was significant in shaping community structure and function in hypoliths. Ecological network analysis showed that most significant co‐occurrences were positive, representing potential synergistic interactions. There were several highly interconnected associations (modules), and specific cyanobacteria were important in driving the modular structure of hypolithic networks. Together, our results suggest that hypolithic cyanobacteria have strong effects on higher trophic levels and ecosystem functioning.     

Long‐term cattle grazing shifts the ecological state of forest soils

Cattle grazing profoundly affects abiotic and biotic characteristics of ecosystems. While most research has been performed on grasslands, the effect of large managed ungulates on forest ecosystems has largely been neglected. Compared to a baseline seminatural state, we investigated how long‐term cattle grazing of birch forest patches affected the abiotic state and the ecological community (microbes and invertebrates) of the soil subsystem. Grazing strongly modified the soil abiotic environment by increasing phosphorus content, pH, and bulk density, while reducing the C:N ratio. The reduced C:N ratio was strongly associated with a lower microbial biomass, mainly caused by a reduction of fungal biomass. This was linked to a decrease in fungivorous nematode abundance and the nematode channel index, indicating a relative uplift in the importance of the bacterial energy‐channel in the nematode assemblages. Cattle grazing highly modified invertebrate community composition producing distinct assemblages from the seminatural situation. Richness and abundance of microarthropods was consistently reduced by grazing (excepting collembolan richness) and grazing‐associated changes in soil pH, Olsen P, and reduced soil pore volume (bulk density) limiting niche space and refuge from physical disturbance. Anecic earthworm species predominated in grazed patches, but were absent from ungrazed forest, and may benefit from manure inputs, while their deep vertical burrowing behavior protects them from physical disturbance. Perturbation of birch forest habitat by long‐term ungulate grazing profoundly modified soil biodiversity, either directly through increased physical disturbance and manure input or indirectly by modifying soil abiotic conditions. Comparative analyses revealed the ecosystem engineering potential of large ungulate grazers in forest systems through major shifts in the composition and structure of microbial and invertebrate assemblages, including the potential for reduced energy flow through the fungal decomposition pathway. The precise consequences for species trophic interactions and biodiversity–ecosystem function relationships remain to be established, however.     

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.     

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β‐1,4‐glucosidase and cellobiohydrolase), chitin (i.e., β‐1,4‐N‐acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram‐negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.     

Does plant community plasticity mediate microbial homeostasis?

Microbial homeostasis—constant microbial element ratios along resource gradients—is a core ecological tenet, yet not all systems display homeostasis. We suggest investigations of homeostasis mechanisms must also consider plant–microbial interactions. Specifically, we hypothesized that ecosystems with strong plant community plasticity to changing resources will have homeostatic microbial communities, with less microbial resource cost, because plants reduce variance in resource stoichiometry. Using long‐term nutrient additions in two ecosystems with differing plant response, we fail to support our hypothesis because although homeostasis appears stronger in the system with stronger plant response, microbial mechanisms were also stronger. However, our conclusions were undermined by high heterogeneity in resources, which may be common in ecosystem‐level studies, and methodological assumptions may be exacerbated by shifting plant communities. We propose our study as a starting point for further ecosystem‐scale investigations, with higher replication to address microbial and soil variability, and improved insight into microbial assimilable resources.     

A new integrative framework for large‐scale assessments of biodiversity and community dynamics,using littoral gastropods and crabs of British Columbia,Canada

Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here, we present and apply an integrative approach that links high‐throughput, multicharacter taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community‐level data set. We collected 1195 gastropods and crabs in British Columbia. First, the General mixed Yule‐coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species‐hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co‐occurrence patterns for nonrandomness using community‐wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species‐hypotheses in community‐level data sets. Nonrandom species co‐occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of carnivorous gastropods and crabs appeared influenced by random processes. Species‐pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co‐occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.