Altered microbial community structure and organic matter composition under elevated CO2 and N fertilization in the duke forest

The dynamics and fate of terrestrial organic matter (OM) under elevated atmospheric CO₂ and nitrogen (N) fertilization are important aspects of long‐term carbon sequestration. Despite numerous studies, questions still remain as to whether the chemical composition of OM may alter with these environmental changes. In this study, we employed molecular‐level methods to investigate the composition and degradation of various OM components in the forest floor (O horizon) and mineral soil (0–15 cm) from the Duke forest free air CO₂ enrichment (FACE) experiment. We measured microbial responses to elevated CO₂ and N fertilization in the mineral soil using phospholipid fatty acid (PLFA) profiles. Increased fresh carbon inputs into the forest floor under elevated CO₂ were observed at the molecular‐level by two degradation parameters of plant‐derived steroids and cutin‐derived compounds. The ratios of fungal to bacterial PLFAs and Gram‐negative to Gram‐positive bacterial PLFAs decreased in the mineral soil with N fertilization, indicating an altered soil microbial community composition. Moreover, the acid to aldehyde ratios of lignin‐derived phenols increased with N fertilization, suggesting enhanced lignin degradation in the mineral soil. ¹H nuclear magnetic resonance (NMR) spectra of soil humic substances revealed an enrichment of leaf‐derived alkyl structures with both elevated CO₂ and N fertilization. We suggest that microbial decomposition of SOM constituents such as lignin and hydrolysable lipids was promoted under both elevated CO₂ and N fertilization, which led to the enrichment of plant‐derived recalcitrant structures (such as alkyl carbon) in the soil.     

Annual burning of a tallgrass prairie inhibits C and N cycling in soil,increasing recalcitrant pyrogenic organic matter storage while reducing N availability

Grassland ecosystems store an estimated 30% of the world's total soil C and are frequently disturbed by wildfires or fire management. Aboveground litter decomposition is one of the main processes that form soil organic matter (SOM). However, during a fire biomass is removed or partially combusted and litter inputs to the soil are substituted with inputs of pyrogenic organic matter (py‐OM). Py‐OM accounts for a more recalcitrant plant input to SOM than fresh litter, and the historical frequency of burning may alter C and N retention of both fresh litter and py‐OM inputs to the soil. We compared the fate of these two forms of plant material by incubating ¹³C‐ and ¹⁵N‐labeled Andropogon gerardii litter and py‐OM at both an annually burned and an infrequently burned tallgrass prairie site for 11 months. We traced litter and py‐OM C and N into uncomplexed and organo‐mineral SOM fractions and CO₂ fluxes and determined how fire history affects the fate of these two forms of aboveground biomass. Evidence from CO₂ fluxes and SOM C:N ratios indicates that the litter was microbially transformed during decomposition while, besides an initial labile fraction, py‐OM added to SOM largely untransformed by soil microbes. Additionally, at the N‐limited annually burned site, litter N was tightly conserved. Together, these results demonstrate how, although py‐OM may contribute to C and N sequestration in the soil due to its resistance to microbial degradation, a long history of annual removal of fresh litter and input of py‐OM infers N limitation due to the inhibition of microbial decomposition of aboveground plant inputs to the soil. These results provide new insight into how fire may impact plant inputs to the soil, and the effects of py‐OM on SOM formation and ecosystem C and N cycling.     

Seed removal in a tropical North American desert: an evaluation of pre‐ and post‐dispersal seed removal in Stenocereus stellatus

• To determine seed removal influence on seed populations, we need to quantify pre‐ and post‐dispersal seed removal. Several studies have quantified seed removal in temperate American deserts, but few studies have been performed in tropical deserts. These studies have only quantified pre‐ or post‐dispersal seed removal, thus underestimating the influence of seed removal. We evaluated pre‐ and post‐dispersal seed removal in the columnar cactus Stenocereus stellatus in a Mexican tropical desert.
• We performed selective exclosure experiments to estimate percentage of seeds removed by ants, birds and rodents during the pre‐ and post‐dispersal phases. We also conducted field samplings to estimate abundance of the most common seed removers.
• Birds (10–28%) removed a higher percentage of seeds than ants (2%) and rodents (1–4%) during pre‐dispersal seed removal. Melanerpes hypopolius was probably the main bird removing seeds from fruits. Ants (62–64%) removed a higher percentage of seeds than birds (34–38%) and rodents (16–30%) during post‐dispersal seed removal. Pogonomyrmex barbatus was probably the main ant removing seeds from soil.
• Birds and ants are the main pre‐ and post‐dispersal seed removers in S. stellatus, respectively. Further studies in other S. stellatus populations and plants with different life forms and fruit types will contribute to evaluate seed removal in tropical American deserts.

     

Nitrogen‐rich microbial products provide new organo‐mineral associations for the stabilization of soil organic matter

Understanding the cycling of C and N in soils is important for maintaining soil fertility while also decreasing greenhouse gas emissions, but much remains unknown about how organic matter (OM) is stabilized in soils. We used nano‐scale secondary ion mass spectrometry (NanoSIMS) to investigate the changes in C and N in a Vertisol and an Alfisol incubated for 365 days with ¹³C and ¹⁵N pulse labeled lucerne (Medicago sativa L.) to discriminate new inputs of OM from the existing soil OM. We found that almost all OM within the free stable microaggregates of the soil was associated with mineral particles, emphasizing the importance of organo‐mineral interactions for the stabilization of C. Of particular importance, it was also found that ¹⁵N‐rich microbial products originating from decomposition often sorbed directly to mineral surfaces not previously associated with OM. Thus, we have shown that N‐rich microbial products preferentially attach to distinct areas of mineral surfaces compared to C‐dominated moieties, demonstrating the ability of soils to store additional OM in newly formed organo‐mineral associations on previously OM‐free mineral surfaces. Furthermore, differences in ¹⁵N enrichment were observed between the Vertisol and Alfisol presumably due to differences in mineralogy (smectite‐dominated compared to kaolinite‐dominated), demonstrating the importance of mineralogy in regulating the sorption of microbial products. Overall, our findings have important implications for the fundamental understanding of OM cycling in soils, including the immobilization and storage of N‐rich compounds derived from microbial decomposition and subsequent N mineralization to sustain plant growth.     

Dispersal alters soil microbial community response to drought

Microbial communities will experience novel climates in the future. Dispersal is now recognized as a driver of microbial diversity and function, but our understanding of how dispersal influences responses to novel climates is limited. We experimentally tested how the exclusion of aerially dispersed fungi and bacteria altered the compositional and functional response of soil microbial communities to drought. We manipulated dispersal and drought by collecting aerially deposited microbes after precipitation events and subjecting soil mesocosms to either filter-sterilized rain (no dispersal) or unfiltered rain (dispersal) and to either drought (25% ambient) or ambient rainfall for 6 months. We characterized community composition by sequencing 16S and ITS rRNA regions and function using community-level physiological profiles. Treatments without dispersal had lower soil microbial biomass and metabolic diversity but higher bacterial and fungal species richness. Dispersal also altered soil community response to drought; drought had a stronger effect on bacterial (but not fungal) community composition, and induced greater functional loss, when dispersal was present. Surprisingly, neither immigrants nor drought-tolerant taxa had higher abundance in dispersal treatments. We show experimentally that natural aerial dispersal rate alters soil microbial responses to disturbance. Changes in dispersal rates should be considered when predicting microbial responses to climate change.     

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long‐term chronosequence

Soil microbial communities are abundant, hyper‐diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper‐diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long‐term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance‐based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long‐term temporal scales.     

Frugivory,Post‐feeding Flights of Frugivorous Birds and the Movement of Seeds in a Brazilian Fragmented Landscape

Habitat fragmentation can break down the movement processes of frugivorous animals, thus influencing the relationship between plants and their seed dispersers by altering the number and identity of seed dispersers, and their relative contribution to seed dispersal. We studied the assemblages of frugivorous birds, their composition, species richness, and visitation rates to fruiting plants growing in the different landscape elements (forest fragments, live fences, and trees isolated in pastures) embedded in a Brazilian fragmented, agricultural landscape. By following the post‐feeding movements of frugivorous birds, we inferred the direction of seed movement from and to each of these landscape elements. Fruiting trees growing at different landscape elements were visited by frugivorous birds at similar rates. Isolated trees attracted a greater and distinct bird assemblage than trees in forest fragments or live fences. Judging by the post‐feeding flights of birds, the seeds of isolated trees were the most likely to reach all the landscape elements considered, but the contribution of isolated trees to the seeds falling in forested habitats or pastures depended on their degree of isolation. A few bird species were able to move widely, visiting fruiting plants in all landscape elements, and promoting long‐distance dispersal for plants. These few birds are of special interest because they are mobile links that connect habitats in fragmented landscapes with their seed dispersal services. Abstract in Spanish is available at http://www.blackwell‐synergy.com/loi/btp .     

Interactive effects of elevated CO2 and nitrogen deposition on fatty acid molecular and isotope composition of above‐ and belowground tree biomass and forest soil fractions

Atmospheric carbon dioxide (CO₂) and reactive nitrogen (N) concentrations have been increasing due to human activities and impact the global carbon (C) cycle by affecting plant photosynthesis and decomposition processes in soil. Large amounts of C are stored in plants and soils, but the mechanisms behind the stabilization of plant‐ and microbial‐derived organic matter (OM) in soils are still under debate and it is not clear how N deposition affects soil OM dynamics. Here, we studied the effects of 4 years of elevated (¹³C‐depleted) CO₂ and N deposition in forest ecosystems established in open‐top chambers on composition and turnover of fatty acids (FAs) in plants and soils. FAs served as biomarkers for plant‐ and microbial‐derived OM in soil density fractions. We analyzed above‐ and belowground plant biomass of beech and spruce trees as well as soil density fractions for the total organic C and FA molecular and isotope (δ¹³C) composition. FAs did not accumulate relative to total organic C in fine mineral fractions, showing that FAs are not effectively stabilized by association with soil minerals. The δ¹³C values of FAs in plant biomass increased under high N deposition. However, the N effect was only apparent under elevated CO₂ suggesting a N limitation of the system. In soil fractions, only isotope compositions of short‐chain FAs (C₁₆₊₁₈) were affected. Fractions of ‘new’ (experimental‐derived) FAs were calculated using isotope depletion in elevated CO₂ plots and decreased from free light to fine mineral fractions. ‘New’ FAs were higher in short‐chain compared to long‐chain FAs (C_20?30), indicating a faster turnover of short‐chain compared to long‐chain FAs. Increased N deposition did not significantly affect the quantity of ‘new’ FAs in soil fractions, but showed a tendency of increased amounts of ‘old’ (pre‐experimental) C suggesting that decomposition of ‘old’ C is retarded by high N inputs.     

Carbon and nitrogen accumulation and microbial activity in Mount St. Helens pyroclastic substrates after 25 years

Lupines (Lupinus lepidus var. lobbii) are important integrators of above and belowground development of Mount St. Helens (1980) pyroclastic substrates because they increase soil organic matter formation and microbial activity and influence other biotic processes. However, basic information is required to understand the unfolding pattern of soil development and to corroborate evidence for increasing rates of organic matter accumulation suggested by earlier work. Soil properties were measured in bare pyroclastic sites without lupines or other plants, under live and under dead L. lepidus. In 2005, pyroclastic substrates had low cation exchange capacity but appeared able to supply sufficient P for plant growth. Soil under live and dead lupines contained higher concentrations of soluble and total C and N, larger, more active microbial communities, more Bradford reactive soil protein and enzymes, and had higher mineralization potentials than bare soil. Comparatively, lupine soil was less dense and had lower C to N ratios and relative respiration rates. Soil microbial biomass-C, determined by substrate-induced respiration, had not increased under lupines since 1990, and was indistinguishable from hot water soluble-C, suggesting microorganisms were a predominant pool of labile-C in these developing soils. Evidence for an important soil glycoprotein, glomalin, in these pyroclastic substrates suggests it can form early during soil development. Concentrations of total C and N under lupines have risen to nearly 4 and 0.4 g kg^?1 respectively since the 1980 eruption, but 2005 data indicate little change since 1997 and imply inputs from lupines into soil are in equilibrium with losses.     

The effects of mineral fertilizer and organic manure on soil microbial community and diversity

The effects of mineral fertilizer (NPK) and organic manure on phospholipid fatty acid profiles and microbial functional diversity were investigated in a long-term (21-year) fertilizer experiment. The experiment included nine treatments: organic manure (OM), organic manure plus fertilizer NPK (OM + NPK), fertilizer NPK (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer N (N), fertilizer P (P), fertilizer K (K), and the control (CK, without fertilization). The original soil was extremely eroded, characterized by low pH and deficiencies of nutrients, particularly N and P. The application of OM and OM + NPK greatly increased crop yields, soil pH, organic C, total N, P and K, available N, P and K content. Crop yields, soil pH, organic C, total N and available N were also clearly increased by the application of mineral NPK fertilizer. The amounts of total PLFAs, bacterial, Gram-negative and actinobacterial PLFAs were highest in the OM + NPK treatment, followed by the OM treatment, whilst least in the N treatment. The amounts of Gram-positive and anaerobic PLFAs were highest in the OM treatment whilst least in the P treatment and the control, respectively. The amounts of aerobic and fungal PLFAs were highest in the NPK treatment whilst least in the N and P treatment, respectively. The average well color development (AWCD) was significantly increased by the application of OM and OM + NPK, and the functional diversity indices including Shannon index (H ^′ ), Simpson index (D) and McIntosh index (U) were also significantly increased by the application of OM and OM + NPK. Principal component analysis (PCA) of PLFA profiles and C source utilization patterns were used to describe changes in microbial biomass and metabolic fingerprints from nine fertilizer treatments. The PLFA profiles from OM, OM + NPK, NP and NPK were significantly different from that of CK, N, P, K and NK, and C source utilization patterns from OM and OM + NPK were clearly different from organic manure deficient treatments (CK, N, P, K, NP, NK 6 and NPK). Stepwise multiple regression analysis showed that total N, available P and soil pH significantly affected PLFA profiles and microbial functional diversity. Our results could provide a better understanding of the importance of organic manure plus balanced fertilization with N, P and K in promoting the soil microbial biomass, activity and diversity and thus enhancing crop growth and production.     

Seed dynamics of resprouting shrubs in grassy woodlands: Seed rain,predators and seed loss constrain recruitment potential

Abstract Measuring the fate of seeds between seed production and seedling establishment is critical in understanding mechanisms of recruitment limitation of plants. We examined seed fates to better understand the recruitment dynamics of four resprouting shrubs from two families (Fabaceae and Epacridaceae) in temperate grassy woodlands. We tested whether: (i) pre‐dispersal seed predation affected seed rain; (ii) post‐dispersal seed predation limited seed bank accumulation; (iii) the size of the seed bank was related to seed size; and (iv) viable seeds accumulated in the soil after seed rain. There was a distinct difference in seed production per plant between plant families with the legumes producing significantly more seeds per individual than the epacrids. Seed viability ranged from 43% to 81% and all viable had seed or fruit coat dormancy broken by heat or scarification. Pre‐dispersal predation by Lepidopteran larvae removed a large proportion of seed from the legume seed rain but not the epacrids. Four species of ants (Notoncus ectatomoides, Pheidole sp., Rhytidoponera tasmaniensis and Iridomyrmex purpureus) were major post‐dispersal seed removers. Overall, a greater percentage of Hardenbergia (38%) and Pultenaea (59%) seeds were removed than the fleshy fruits of Lissanthe (14%) or Melichrus (0%). Seed bank sizes were small (<15 seeds m^?2) relative to the seed rain and no significant accumulation of seed in the soil was detected. Lack of accumulation was attributed to seed predation as seed decay was considered unlikely and no seed germination was observed in our study sites. Our study suggests that seed predation is a key factor contributing to seed‐limited recruitment in grassy woodland shrubs by reducing the number of seeds stored in the soil.     

Bird Perches Increase Forest Seeds on Puerto Rican Landslides

Abstract Landslides result in the loss of vertical vegetative structure, soil nutrients, and the soil seed bank. These losses impede timely recovery of tropical forest communities. In this study we added bird perches to six Puerto Rican landslides with three types of surfaces (bare, climbing fern, grass) in an effort to facilitate inputs of forest seeds through bird dispersal and to accelerate plant succession. Numbers of bird‐dispersed forest seeds were significantly higher in plots beneath introduced perches than in control plots. Perches did not increase forest seedling densities compared with control plots. Seven different species of birds were observed on introduced perches. Because 99% of the seed inputs to controls and perch plots in the six landslides were wind‐dispersed seeds (mostly graminoids), perches can improve landslide restoration if woody plants establish and shade out the dominant graminoid and climbing fern ground cover. Although increasing seed inputs from forest species is a critical step in accelerating revegetation of landslides, we suggest that supplemental restoration techniques be applied in addition to bird perches to promote forest recovery.     

A Molecular Comparison of Plumage and Soil Bacteria Across Biogeographic,Ecological, and Taxonomic Scales

We used molecular methods to determine the microbial community of soil and avian plumage across biogeographic, ecological, and taxonomic scales. A total of 17 soil and 116 feather samples were collected from five avian species across multiple habitat types within one Neotropical and one temperate locality. Hypotheses regarding patterns of microbial composition relative to acquisition and dispersal of plumage bacteria in the ecosystem were tested by comparing microbial communities within and between soil and plumage. Samples from the plumage of American Redstarts (Setophaga ruticilla) were collected across both habitat types and geographic scales for intraspecific comparisons. The microbial diversity in avian plumage was moderately diverse and was dominated by Pseudomonas species. Despite a highly significant individual bird effect on microbial composition of the plumage, we detected significant biogeographic and type of habitat effects. Pseudomonas species were more abundant on the temperate site when all avian species were included in the analysis, and Bacillus subtilis and Xanthomonas groups were more abundant on the Neotropical site for redstarts alone. However, 16S rDNA sequence libraries were not significantly different between Jamaican and Maryland redstarts. Biogeographic and habitat effects were significant and more pronounced for soil samples indicating lower dispersal of soil microbiota. We detected a significant difference between soil and plumage microbial communities suggesting that soil plays a small role in plumage bacterial acquisition. Our results suggest bacterial communities on the plumage of birds are dynamic and may change at different stages in a bird’s annual cycle.     

Soil Water Content and Organic Carbon Availability Are Major Determinants of Soil Microbial Community Composition

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (–C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.     

Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales

The extent to which the distribution of soil bacteria is controlled by local environment vs. spatial factors (e.g. dispersal, colonization limitation, evolutionary events) is poorly understood and widely debated. Our understanding of biogeographic controls in microbial communities is likely hampered by the enormous environmental variability encountered across spatial scales and the broad diversity of microbial life histories. Here, we constrained environmental factors (soil chemistry, climate, above‐ground plant community) to investigate the specific influence of space, by fitting all other variables first, on bacterial communities in soils over distances from m to 10² km. We found strong evidence for a spatial component to bacterial community structure that varies with scale and organism life history (dispersal and survival ability). Geographic distance had no influence over community structure for organisms known to have survival stages, but the converse was true for organisms thought to be less hardy. Community function (substrate utilization) was also shown to be highly correlated with community structure, but not to abiotic factors, suggesting nonstochastic determinants of community structure are important Our results support the view that bacterial soil communities are constrained by both edaphic factors and geographic distance and further show that the relative importance of such constraints depends critically on the taxonomic resolution used to evaluate spatio‐temporal patterns of microbial diversity, as well as life history of the groups being investigated, much as is the case for macro‐organisms.     

Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils

A central aim of this microbial ecology research was to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modelling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co‐occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.     

环境选择和扩散限制驱动温带森林土壤细菌群落的构建

环境选择和扩散限制是生态系统中生物群落构建的两个基本过程,而两者相对作用的大小因研究尺度、群落属性和类型等有所不同.目前对温带亚高山森林土壤微生物群落构建的驱动因子和机制尚缺乏了解.本文利用PCR-DGGE技术研究庞泉沟自然保护区内5种典型森林包括华北落叶松林、青杄林、白杄林、油松林以及桦树林的6个森林土壤细菌群落(Lp MC1、Lp MC2、Pw MC、Pm MC、Pt MC、BMC)的结构特征及其影响因素,分析细菌群落结构与环境因子的相关性,以及土壤因子、植被和空间因素对细菌群落结构的影响.结果表明:研究区各样地土壤细菌群落的结构和生物多样性具有显著差异,低海拔落叶松和油松土壤细菌群落多样性较高(20条带),白杄林土壤细菌群落(13条带)多样性最低,高海拔落叶松土壤细菌群落多样性最高;土壤环境因子,如pH、土壤含水量、总碳、总氮、土壤有机质、速效磷以及土壤酶活性与土壤细菌群落多样性和结构显著相关;样地土壤细菌群落的beta多样性与群落的空间距离呈显著相关,表明扩散限制对群落结构具有一定的影响;方差分解分析结果显示,6个样地细菌群落结构的驱动因素大小依次为土壤因子(0.27)、空间因素(0.19)和植被(0.15);将区域土壤微生物作为"源群落",微宇宙试验结果显示,土壤因子是细菌群落结构形成的主要驱动力(0.35),同时源群落丰富的物种多样性对微宇宙土壤细菌群落结构具有显著影响.总之,在局域尺度下,环境选择对温带森林土壤细菌群落结构动态和多样性发挥主导作用,地理距离对群落结构具有显著影响,即确定性过程和随机过程共同决定局域森林土壤细菌群落结构,前者占主导地位.对于土壤细菌群落而言,扩散群落的组成和结构受到源群落的多样性特征和环境因子的双重影响.     

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Microbial communities in plant roots provide critical links between above‐ and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities, we designed a trap‐plant bioassay experiment. Replicate Populus, Quercus and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of four loci (i.e., 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.     

Biogeographical patterns of abundant and rare bacterial biospheres in paddy soils across East Asia

Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub-communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub-communities consistently displayed significant distance–decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub-communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%–49.78%) and average annual air temperature (16.59%–46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils.     

Soil Properties and Spatial Processes Influence Bacterial Metacommunities within a Grassland Restoration Experiment

Metacommunity theory proposes that a collection of local communities are linked by dispersal and the resulting compositions are a product of both niche‐based (species sorting) and spatial processes. Determining which of these factors is most important in different habitats can provide insight into the regulation of community assembly. To date, the metacommunity organization of heterotrophic soil bacteria is largely unknown. Spatial variation of soil bacterial communities could arise from (1) the resource heterogeneity produced by plant communities through root exudation and/or litter inputs; (2) the heterogeneity of soil environmental properties; and (3) pure spatial processes, including dispersal limitation and stochastic assembly. Understanding the relative importance of these factors for soil bacterial community structure and function could increase our ability to restore soil communities. We utilized an ongoing tallgrass prairie restoration experiment in northeastern Kansas to assess if restoring native plant communities produced changes in bacterial communities 6 years after restoration. We further examined the relative importance of the spatial heterogeneity of plant communities, soil properties, and pure spatial effects for bacterial community structure in the old‐field restoration site. We found that soil bacterial communities were not influenced by plant restoration, but rather, by the local heterogeneity of soil environmental properties (16.9% of bacterial community variation) and pure spatial effects (11.1%). This work also stresses the idea that restoring bacterial communities can take many years to accomplish due to the inherent changes that occur to the soil after cultivation and the time it takes for the re‐establishment of soil quality.