Temporal variability in soil microbial communities across land-use types

Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.     

Agricultural land-use affects the nutritional quality of stream microbial communities

We investigated how the lipid composition (fatty acids and sterols) of benthic microbial mats, which represent an important basal food resource for stream food webs, differs between tropical streams located in protected pristine and agricultural Cerrado savannah areas. The total microbial biomass and lipid composition differed significantly between pristine and agricultural streams in parallel with differences in water quality and hydrodynamic characteristics. Agricultural streams exhibited lower total biomass of benthic microbial mats than pristine streams. However, the higher concentrations of essential polyunsaturated fatty acids, such as linoleic acid (LIN, 18:2ω6), α-linolenic acid (ALA, 18:3ω3), and eicosapentaenoic acid (EPA, 20:5ω3), that were observed in agricultural streams suggest enhanced lipid complexity and a higher nutritional quality of the microbial community relative to pristine streams. Meanwhile, pristine stream microbial communities had higher total concentrations of saturated fatty acids and cholesterol than those of agricultural streams, reflecting their heterotrophic microbial communities. Moreover, stream morphotype and associated differences in the hydrodynamic characteristics affected the community composition and thereby also the lipid composition of microbial mats. Land-use-induced changes in the total biomass and lipid composition of microbial communities may affect the trophic transfer of energy in stream food webs, leading to changes in the composition and productivity of primary consumers and their predators, and thereby affecting stream ecosystem functioning.     

Response of collembolan communities to land-use change and grassland succession

This study focuses on the long-term changes of collembolan communities occurring after the conversion of arable land to managed grassland. We analysed collembolan communities at grassland sites of different age that had been gradually converted over a period of 50 yr. Abundance and biomass responded rapidly and very positively to the conversion of arable land to grassland, while species richness was not affected. Collembolan assemblages changed only little during grassland maturation. The impact of land-use change on community structure was more obvious at the functional level because the colonization processes observed in our study mostly relied on hemiedaphic species. Vegetation and soil parameters were good predictors of collembolan community structure during development of managed grassland. The present study demonstrated that past landscape patterns and processes like land-use conversion and subsequent succession had a considerable impact on the present day pattern of species richness and community composition of Collembola within a landscape. Our results strongly differ from those obtained for other invertebrate groups, highlighting on the one hand the very diverse reactions of invertebrates to a common factor, and on the other hand the need to survey more than one taxa in order to draw conclusions on effects of land-use change on faunistic communities.     

Heterotrophic microbial communities use ancient carbon following glacial retreat

When glaciers retreat they expose barren substrates that become colonized by organisms, beginning the process of primary succession. Recent studies reveal that heterotrophic microbial communities occur in newly exposed glacial substrates before autotrophic succession begins. This raises questions about how heterotrophic microbial communities function in the absence of carbon inputs from autotrophs. We measured patterns of soil organic matter development and changes in microbial community composition and carbon use along a 150-year chronosequence of a retreating glacier in the Austrian Alps. We found that soil microbial communities of recently deglaciated terrain differed markedly from those of later successional stages, being of lower biomass and higher abundance of bacteria relative to fungi. Moreover, we found that these initial microbial communities used ancient and recalcitrant carbon as an energy source, along with modern carbon. Only after more than 50 years of organic matter accumulation did the soil microbial community change to one supported primarily by modern carbon, most likely from recent plant production. Our findings suggest the existence of an initial stage of heterotrophic microbial community development that precedes autotrophic community assembly and is sustained, in part, by ancient carbon.     

Traits of butterfly communities change from specialist to generalist characteristics with increasing land-use intensity

Land-use intensification leads to species loss and shifts in community composition, but only few studies examine how these dynamics affect ecological and life-history traits. We thus investigated whether ecological and life-history traits differ between butterfly communities of grasslands with different land-use intensity. We conducted butterfly transect surveys in 137 grassland sites in three regions of Germany and compiled 10 species-specific ecological and life-history traits from the literature. These traits are associated with food plant specialisation, dispersal, distribution, reproduction and development. We calculated a land-use intensity gradient based on the amount of fertilise mowing frequency and grazing intensity. We analysed differences of traits characteristics between butterfly communities along the land-use intensity gradient in a fourth-corner analysis, thus considering correlations between traits. Six ecological and life-history traits changed from characteristics associated with specialists to such associated with generalists with increasing land-use intensity. These traits characteristics in intensified grasslands were: high dispersal propensity, large distribution range, low population density, more than one generation per year, hibernation in a more advanced developmental stage and a long flight period. The functional homogenisation of the butterfly communities with changes from specialist to generalist trait characteristics with increasing land-use intensity may have severe consequences for ecosystem functioning and services.     

Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis

In completely insular microbial communities, evolution of community structure cannot be shaped by the immigration of new members. In addition, when those communities are run in steady state, the influence of environmental factors on their assembly is reduced. Therefore, one would expect similar community structures under steady-state conditions. Yet, in parallel setups, variability does occur. To reveal ecological mechanisms behind this phenomenon, five parallel reactors were studied at the single-cell level for about 100 generations and community structure variations were quantified by ecological measures. Whether community variability can be controlled was tested by implementing soft temperature stressors as potential synchronizers. The low slope of the lognormal rank-order abundance curves indicated a predominance of neutral mechanisms, i.e., where species identity plays no role. Variations in abundance ranks of subcommunities and increase in inter-community pairwise β-diversity over time support this. Niche differentiation was also observed, as indicated by steeper geometric-like rank-order abundance curves and increased numbers of correlations between abiotic and biotic parameters during initial adaptation and after disturbances. Still, neutral forces dominated community assembly. Our findings suggest that complex microbial communities in insular steady-state environments can be difficult to synchronize and maintained in their original or desired structure, as they are non-equilibrium systems.     

间作栽培对连作马铃薯根际土壤微生物群落的影响

连作严重影响了作物的产量和品质,而土壤微生物群落结构与功能对土壤生态系统和植物健康至关重要。以连作10a土壤为基质,单作马铃薯为对照,采用磷脂脂肪酸(Phospholipid fatty acids)、BIOLOGA技术和真菌形态学鉴定方法,研究了玉米、蚕豆与马铃薯间作模式下土壤微生物群落结构、功能和丛植菌根(Arbuscular Mycorrhizal)真菌对土壤环境变化的响应。结果表明:间作调控下,马铃薯根际土壤微生物主要类群结构发生显著改变;玉米间作马铃薯,土壤微生物群落总生物量降低,但群落功能多样性提高,促进了以羧酸类、多聚化合物、芳香类化合物、氨基酸类化合物为碳源的微生物类群代谢活性增强;蚕豆间作增加了土壤微生物总生物量,仅促进了以碳水化合物为碳源的微生物类群代谢活性。间作改变了作物根际土壤AM真菌的种、属数,AM真菌多样性降低,优势种由明球囊霉、地球囊霉转变为玉米间作体系里的福摩萨球囊霉、球泡球囊霉;蚕豆间作体系里福摩萨球囊霉和疣状无梗囊霉是优势种。间作栽培下AM真菌优势种群的变化可能受植物间的共生关系、微生物结构与功能等因素的制约。间作条件下,玉米显著影响了马铃薯根际土壤微生物群落功能多样性,而蚕豆则显著改变了微生物群落结构多样性;玉米、蚕豆对马铃薯根际土壤微生物群落功能与结构变化的影响不同步;间作调控后持续的土壤微生物群落结构与功能观察才有助于解释土壤微生物结构变化引起的功能响应。     

Exploring stream communities in a tropical biodiversity hotspot: biodiversity,regional occupancy,niche characteristics and environmental correlates

Exploring and describing biodiversity and the mechanisms structuring it is fundamental to advancing ecology. This is particularly pertinent in understudied biogeographical regions, such as the Afrotropics, that are characterised by strong seasonal climatic shifts. We investigated the characteristics of stream biodiversity in the Niger Delta region of Nigeria, a tropical biodiversity hotspot, by examining patterns in 20 stream invertebrate communities across both the wet and dry seasons. For this, we took a multi-faceted approach accounting for the three levels of biodiversity (α, β and γ), including partitioning the nestedness and turnover components of β diversity, regional occupancy-abundance patterns, niche characteristics, and the environmental drivers of community structure. α diversity was low in these streams, with strong turnover between sites leading to high β diversity contributing to regional biodiversity, but there was little variation in communities between seasons. The proportion of sites occupied by taxa declined with increasing niche position, and decreasing niche breadth. Occupancy was predicted well by a combination of these two factors (niche position and breadth), but not mean local abundance, as the abundance-occupancy link was an upper-limit unimodal relationship. On average, community structure was linked more strongly to environmental variables in the wet season. Our findings demonstrate the clear role of spatial, but not temporal, turnover in assemblages, which likely reflects the environmental heterogeneity of this region. This is further supported by the fact that regional occupancy was mostly related to niche characteristics, particularly niche position. We emphasise the importance of continued basic and applied ecological work in this important biogeographic region to enable better protection of its biodiversity.     

Effect of long-term application of agrotechnical techniques and crops on soil microbial communities

Effects of long-term application of various fertilizers and crops on soil microbiomes in a long-term field experiment were investigated using the library of the 16S rRNA gene sequences obtained by highthroughput sequencing of the total DNA. The communities exhibited high diversity, with 655 microbial genera belonging to 34 phyla detected (31 bacterial and 3 archaeal ones). For analysis of the effect of the studied factors on community structure, a linear model was developed in order to simplify interpretation of the data of high-throughput sequencing and to obtain biologically important information. Liming was shown to modulate the effect of mineral fertilizers on the structure of microbial populations. The differences in the structure and alpha-diversity of microbial communities were shown to depend more on the crops and liming than on the fertilizers applied. Interaction between the crop factor and liming expressed as an ambiguous effect of liming on the microbiome in the presence of different plants was reliably demonstrated. Thus, in the case of barley and clover, liming resulted in increased taxonomic diversity of the community, while in the case of potato and flax it had an opposite effect.     

Landscape fragmentation affects responses of avian communities to climate change

Forecasting the consequences of climate change is contingent upon our understanding of the relationship between biodiversity patterns and climatic variability. While the impacts of climate change on individual species have been well‐documented, there is a paucity of studies on climate‐mediated changes in community dynamics. Our objectives were to investigate the relationship between temporal turnover in avian biodiversity and changes in climatic conditions and to assess the role of landscape fragmentation in affecting this relationship. We hypothesized that community turnover would be highest in regions experiencing the most pronounced changes in climate and that these patterns would be reduced in human‐dominated landscapes. To test this hypothesis, we quantified temporal turnover in avian communities over a 20‐year period using data from the New York State Breeding Atlases collected during 1980–1985 and 2000–2005. We applied Bayesian spatially varying intercept models to evaluate the relationship between temporal turnover and temporal trends in climatic conditions and landscape fragmentation. We found that models including interaction terms between climate change and landscape fragmentation were superior to models without the interaction terms, suggesting that the relationship between avian community turnover and changes in climatic conditions was affected by the level of landscape fragmentation. Specifically, we found weaker associations between temporal turnover and climatic change in regions with prevalent habitat fragmentation. We suggest that avian communities in fragmented landscapes are more robust to climate change than communities found in contiguous habitats because they are comprised of species with wider thermal niches and thus are less susceptible to shifts in climatic variability. We conclude that highly fragmented regions are likely to undergo less pronounced changes in composition and structure of faunal communities as a result of climate change, whereas those changes are likely to be greater in contiguous and unfragmented habitats.     

Antarctic nematode communities: observed and predicted responses to climate change

The rapidly changing climate in Antarctica is impacting the ecosystems. Since records began, climate changes have varied considerably throughout Antarctica with both positive and negative trends in temperatures and precipitation observed locally. However, over the course of this century a more directional increase in both temperature and precipitation is expected to occur throughout Antarctica. The soil communities of Antarctica are considered simple with most organisms existing at the edge of their physiological capabilities. Therefore, Antarctic soil communities are expected to be particularly sensitive to climate changes. However, a review of the current literature reveals that studies investigating the impact of climate change on soil communities, and in particular nematode communities, in Antarctica are very limited. Of the few studies focusing on Antarctic nematode communities, long-term monitoring has shown that nematode communities respond to changes in local climate trends as well as extreme (or pulse) events. These results are supported by in situ experiments, which show that nematode communities respond to both temperature and soil moisture manipulations. We conclude that the predicted climate changes are likely to exert a strong influence on nematode communities throughout Antarctica and will generally lead to increasing abundance, species richness, and food web complexity, although the opposite may occur locally. The degree to which local communities respond will depend on current conditions, i.e., average temperatures, soil moisture availability, vegetation or more importantly the lack thereof, and the local species pool in combination with the potential for new species to colonize.     

冻土甲烷循环微生物群落及其对全球变化的响应

冻土是陆地生态系统中最容易受到全球气候变化影响的碳库,既发挥着碳源又起着碳汇的作用。人们非常关注贮存于冻土中有机碳的最终归宿,是因为全球气候变暖会加快冻土的解冻,释放更多的温室气体（二氧化碳和甲烷）到大气中,从而进一步加剧温室效应。据估计每年从北半球冻原陆地生态系统释放进入大气的甲烷约占全球自然界释放甲烷总量的25%。研究证实冻土生物源甲烷的产生和消耗分别由耐(嗜)低温的产甲烷菌(methanogens)和甲烷氧化菌(methanotrophs)介导。鉴于冻土甲烷循环对全球甲烷平衡的显著作用以及在冻土生物地球化学循环中的重要功能,对介导冻土甲烷循环的产甲烷菌和甲烷氧化菌的研究将有助于更好地评估冻土生态系统对全球气候变化的响应和影响,本文就冻土甲烷循环过程、产甲烷菌、甲烷氧化菌的群落结构、活动、生态功能及其对气候和环境变化的响应机制的最新研究进行综述,以期为我国开展冻土甲烷循环机理研究提供支持。     

Biogeographic variation in behavioral and morphological responses to predation risk

The expression of prey antipredator defenses is often related to ambient consumer pressure, and prey express greater defenses under intense consumer pressure. Predation is generally greater at lower latitudes, and antipredator defenses often display a biogeographic pattern. Predation pressure may also vary significantly between habitats within latitudes, making biogeographic patterns difficult to distinguish. Furthermore, invasive predators may also influence the expression of prey defenses in ecological time. The purpose of this study was to determine how these factors influence the strength of antipredator responses. To assess patterns in prey antipredator defenses based upon geographic range (north vs. south), habitat type (wave-protected vs. wave-exposed shores), and invasive predators, we examined how native rock (Cancer irroratus) and invasive green (Carcinus maenas) crab predators influence the behavioral and morphological defenses of dogwhelk (Nucella lapillus) prey from habitats that differ in wave exposure across an ~230 km range within the Gulf of Maine. The expression of behavioral and morphological antipredatory responses varied according to wave exposure, geographic location, and predator species. Dogwhelks from areas with an established history with green crabs exhibited the largest behavioral and morphological antipredator responses to green crabs. Dogwhelk behavioral responses to rock crabs did not vary between habitats or geographic regions, although morphological responses were greater further south where predation pressure was greatest. These findings suggest that dogwhelk responses to invasive and native predators vary according to geographic location and habitat, and are strongly affected by ambient predation pressure due to the invasion history of an exotic predator.     

Bar-coded pyrosequencing reveals the responses of PBDE-degrading microbial communities to electron donor amendments

Polybrominated diphenyl ethers (PBDEs) can be reductively degraded by microorganisms under anaerobic conditions. However, little is known about the effect of electron donors on microbial communities involved in PBDEs degradation. Here we employed 454 Titanium pyrosequencing to examine the phylogenetic diversity, composition, structure and dynamics of microbial communities from microcosms under the conditions of different electron donor amendments. The community structures in each of the five alternate electron donor enrichments were significantly shifted in comparison with those of the control microcosm. Commonly existing OTUs between the treatment and control consortia increased from 5 to 17 and more than 50% of OTUs increased around 13.7 to 186 times at least in one of the microcosms after 90-days enrichment. Although the microbial communities at different taxonomic levels were significantly changed by different environmental variable groups in redundancy analysis, significant correlations were observed between the microbial communities and PBDE congener profiles. The lesser-brominated PBDE congeners, tri-BDE congener (BDE-32) and hexa-BDE, were identified as the key factors shaping the microbial community structures at OTU level. Some rare populations, including the known dechlorinating bacterium, Dehalobacter, showed significant positive-correlation with the amounts of PBDE congeners in the consortia. The same results were also observed on some unclassified bacteria. These results suggest that PBDEs-degrading microbial communities can be successfully enriched, and their structures and compositions can be manipulated through adjusting the environmental parameters.