Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere

The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.     

Environmental exposure more than plastic composition shapes marine microplastic-associated bacterial communities in Pacific versus Caribbean field incubations

Microplastics have arisen as a global threat to marine ecosystems. In this study, we explored the role that plastic polymer type, incubation time and geographic location have on shaping the microbial community adhered to the microplastics, termed the plastisphere. We performed detailed bacterial plastisphere community analyses on microplastics of six different household plastic polymers, serving as proxies of secondary microplastics, incubated for 6 weeks in coastal Pacific waters. These bacterial communities were compared to the plastisphere communities grown on identical microplastic particles incubated in the coastal Caribbean Sea at Bocas del Toro, Panama. Ribosomal gene sequencing analyses revealed that bacterial community composition did not exhibit a significant preference for plastic type at either site but was instead driven by the incubation time and geographic location. We identified a ‘core plastisphere’ composed of 57 amplicon sequence variants common to all plastic types, incubation times and locations, with possible synergies between taxa. This study contributes to our understanding of the importance of geography in addition to exposure time, in the composition of the plastisphere.     

Soil plastispheres as hotspots of antibiotic resistance genes and potential pathogens

In the Anthropocene, increasing pervasive plastic pollution is creating a new environmental compartment, the plastisphere. How the plastisphere affects microbial communities and antibiotic resistance genes (ARGs) is an issue of global concern. Although this has been studied in aquatic ecosystems, our understanding of plastisphere microbiota in soil ecosystems remains poor. Here, we investigated plastisphere microbiota and ARGs of four types of microplastics (MPs) from diverse soil environments, and revealed effects of manure, temperature, and moisture on them. Our results showed that the MPs select for microbial communities in the plastisphere, and that these plastisphere communities are involved in diverse metabolic pathways, indicating that they could drive diverse ecological processes in the soil ecosystem. The relationship within plastisphere bacterial zero-radius operational taxonomic units (zOTUs) was predominantly positive, and neutral processes appeared to dominate community assembly. However, deterministic processes were more important in explaining the variance in ARGs in plastispheres. A range of potential pathogens and ARGs were detected in the plastisphere, which were enriched compared to the soil but varied across MPs and soil types. We further found that the addition of manure and elevation of soil temperature and moisture all enhance ARGs in plastispheres, and potential pathogens increase with soil moisture. These results suggested that plastispheres are habitats in which an increased potential pathogen abundance is spatially co-located with an increased abundance of ARGs under global change. Our findings provided new insights into the community ecology of the microbiome and antibiotic resistome of the soil plastisphere.Subject terms: Microbial ecology, Environmental sciences     

Contribution of stochastic processes to the microbial community assembly on field-collected microplastics

A growing body of evidence suggests that microplastics may be colonized with a unique microbiome, termed ‘plastisphere’, in aquatic environments. However, the deep mechanisms (deterministic and/or stochastic processes) underlying the community assembly on microplastics are still poorly understood. Here, we took the estuary of Hangzhou Bay (Zhejiang, China) as an example and examined the assembly mechanisms of bacterial communities in water and microplastic samples. Results from high-throughput sequencing showed that Proteobacteria, Firmicutes, and Actinobacteria were the dominant phyla across all samples. Additionally, microorganisms from plastisphere and planktonic communities exhibited contrasting taxonomic compositions, with greater within-group variation for microplastic samples. The null model analysis indicated the plastisphere bacterial communities were dominantly driven by the stochastic process of drift (58.34%) and dispersal limitation (23.41%). The normalized stochasticity ratio (NST) also showed that the community assembly on microplastics was more stochastic (NST > 50%). Based on the Sloan neutral community model, the migration rate for plastisphere communities (0.015) was significantly lower than that for planktonic communities (0.936), potentially suggesting that it is the stochastic balance between loss and gain of bacteria (e.g., stochastic births and deaths) critically shaping the community assembly on microplastics and generating the specific niches. This study greatly enhanced our understanding of the ecological patterns of microplastic-associated microbial communities in aquatic environments.     

Core taxa underpin soil microbial community turnover during secondary succession

Understanding the processes that underpin the community assembly of bacteria is a key challenge in microbial ecology. We studied soil bacterial communities across a large-scale successional gradient of managed and abandoned grasslands paired with mature forest sites to disentangle drivers of community turnover and assembly. Diversity partitioning and phylogenetic null-modelling showed that bacterial communities in grasslands remain compositionally stable following abandonment and secondary succession but they differ markedly from fully afforested sites. Zeta diversity analyses revealed the persistence of core microbial taxa that both reflected and differed from whole-scale community turnover patterns. Differences in soil pH and C:N were the main drivers of community turnover between paired grassland and forest sites and the variability of pH within successional stages was a key factor related to the relative dominance of deterministic assembly processes. Our results indicate that grassland microbiomes could be compositionally resilient to abandonment and secondary succession and that the major changes in microbial communities between grasslands and forests occur fairly late in the succession when trees have established as the dominant vegetation. We also show that core taxa may show contrasting responses to management and abandonment in grasslands.     

The scale dependence of fungal community distribution in paddy soil driven by stochastic and deterministic processes

Fungal communities play important roles in terrestrial ecosystem functioning. Unraveling the relative importance of stochastic versus deterministic processes in shaping biogeographic patterns of fungal communities has long been a challenge in microbial ecology, owing to high biodiversity and difficulties in identifying fungal taxa. Using a unique anthropogenic system of geographically isolated paddy ‘islands’, we collected 198 soil samples with a spatially explicit design to examine how ecological processes shaped fungal biogeographic patterns. Fungal community structure showed scale-dependent distance-decay relationships. Stochastic processes (dispersal and drift) contributed more to community assembly than deterministic processes (selection) at the local scale, which was largely attributed to drift. In contrast, deterministic processes contributed more to community assembly than stochastic processes at the regional scale, with soil dissolved organic carbon being the most important measured factor. Collectively, scale dependence of fungal biogeographical patterns in paddy soils is influenced by differential contribution of deterministic and stochastic processes.     

Microplastics reduce soil microbial network complexity and ecological deterministic selection

Microplastics have been proposed as emerging threats for terrestrial systems as they may potentially alter the physicochemical/biophysical soil environments. Due to the variety of properties of microplastics and soils, the microplastic-induced effects in soil ecosystems are greatly manifold. Here, we studied effects of three polymer microplastics (polyamide-6, polyethylene, and polyethylene terephthalate) on soil properties with four different soil types. The success patterns, interaction relationships, and assembly processes of soil bacterial communities were also studied. Microplastics have the potential to promote CO₂ emissions and enhance the soil humification. Even though microplastics did not significantly alter the diversity and composition of the soil microbial community, the application of microplastics decreased the network complexity and stability, including network size, connectivity, and the number of module and keystone species. The bacterial community assembly was governed by deterministic selection (77.3%–90.9%) in all treatments, while microplastics increased the contribution of stochastic processes from 9.1% in control to 13.6%–22.7%. The neutral model results also indicated most of the bacterial taxa were present in the predicted neutral region (approximately 98%), suggesting the importance of stochastic processes. These findings provided a fundamental insight in understanding the effects of microplastics on soil ecosystems.     

盐度对滨海土壤细菌多样性和群落构建过程的影响

滨海盐土是重要的农业土地后备资源。微生物是土壤中物质循环的关键动力,然而盐度对土壤微生物群落特征影响的研究还很缺乏。本研究采集滨海地区的土壤样品,研究非盐、轻盐和高盐3组不同盐度对土壤细菌数量、多样性和群落构建的影响。结果表明: 与非盐和轻盐土壤相比,高盐土壤的脱氢酶活性和细菌数量显著降低,而细菌α多样性没有变化,细菌群落结构发生分异。利用零模型反演群落构建过程,发现盐度是细菌群落构建过程的主控因子,盐度主导的高确定性过程控制了滨海盐土细菌的群落结构。说明在现有的盐度范围内,高盐土壤中同样含有丰富的微生物种质资源,具有盐土改良的生物学基础,然而由于高确定性的群落构建机制,外源物种很难定殖于滨海盐土。因此,在利用微生物技术改良滨海盐土时,应尽可能筛选耐盐的土著菌种,提高定殖效率。     

Movement of protistan trophic groups in soil–plant continuums

Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil–plant continuums. However, the drivers of community structure, assembly mechanisms, co-occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter-kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co-occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen–consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil–plant continuums, which is fundamental to the regulation of soil–plant microbiomes and maintenance of environmental and human health.     

Microbes and microplastics: Community shifts along an urban coastal contaminant gradient

Plastic substrates introduced to the environment during the Anthropocene have introduced new pathways for microbial selection and dispersal. Some plastic-colonising microorganisms have adapted phenotypes for plastic degradation (selection), while the spatial transport (dispersal) potential of plastic colonisers remains controlled by polymer-specific density, hydrography and currents. Plastic-degrading enzyme abundances have recently been correlated with concentrations of plastic debris in open ocean environments, making it critical to better understand colonisation of hydrocarbon degraders with plastic degradation potential in urbanised watersheds where plastic pollution often originates. We found that microbial colonisation by reputed hydrocarbon degraders on microplastics (MPs) correlated with a spatial contaminant gradient (New York City/Long Island waterways), polymer types, temporal scales, microbial domains and putative cell activity (DNA vs. RNA). Hydrocarbon-degrading taxa enriched on polyethylene and polyvinyl chloride substrates relative to other polymers and were more commonly recovered in samples proximal to New York City. These differences in MP colonisation could indicate phenotypic adaptation processes resulting from increased exposure to urban plastic runoff as well as differences in carbon bioavailability across polymer types. Shifts in MP community potential across urban coastal contaminant gradients and polymer types improve our understanding of environmental plastic discharge impacts toward biogeochemical cycling across the global ocean.     

Neutral Models of Microbiome Evolution

There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes). Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these microbiomes may have evolved. In this paper, we develop an agent-based framework to study the dynamics of microbiome evolution. Our framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled. Most importantly, our framework also incorporates a Wright-Fisher genealogical model of hosts, so that the dynamics of microbiome evolution is studied on an evolutionary timescale. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes: the greater the parental contribution, the less diverse the microbiomes. In contrast, even when there is only a very small contribution from a constant environmental pool, microbial communities can remain highly diverse. Finally, we show that our models may be used to construct hypotheses about the types of processes that operate to assemble microbiomes over evolutionary time.     

Mechanisms of soil bacterial and fungal community assembly differ among and within islands

The study of islands has made substantial contributions to the development of evolutionary and ecological theory. However, we know little about microbial community assembly on islands. Using soil microbial data collected from 29 lake islands and nearby mainland, we examined the assembly mechanisms of soil bacterial and fungal communities among and within islands. We found that deterministic processes, especially homogeneous selection, tended to be more important in shaping the assembly of soil bacterial communities among islands, while stochastic processes tended to be more important within islands. Moreover, increasing island area increased the importance of homogeneous selection, but reduced the importance of variable selection, for soil bacterial community assembly within islands. By contrast, stochastic processes tended to dominate soil fungal community assembly both among and within islands, with dispersal limitation playing a more important role within than among islands. Our results highlight the scale- and taxon-dependence of insular soil microbial community assembly, suggesting that spatial scale should be explicitly considered when evaluating the influences of habitat fragmentation on soil microbial communities.     

Distinct patterns of soil bacterial and fungal community assemblages in subtropical forest ecosystems under warming

Climate change globally affects soil microbial community assembly across ecosystems. However, little is known about the impact of warming on the structure of soil microbial communities or underlying mechanisms that shape microbial community composition in subtropical forest ecosystems. To address this gap, we utilized natural variation in temperature via an altitudinal gradient to simulate ecosystem warming. After 6 years, microbial co-occurrence network complexity increased with warming, and changes in their taxonomic composition were asynchronous, likely due to contrasting community assembly processes. We found that while stochastic processes were drivers of bacterial community composition, warming led to a shift from stochastic to deterministic drivers in dry season. Structural equation modelling highlighted that soil temperature and water content positively influenced soil microbial communities during dry season and negatively during wet season. These results facilitate our understanding of the response of soil microbial communities to climate warming and may improve predictions of ecosystem function of soil microbes in subtropical forests.     

Selection on soil microbiomes reveals reproducible impacts on plant function

Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools.     

A Coexisting Fungal-Bacterial Community Stabilizes Soil Decomposition Activity in a Microcosm Experiment

How diversity influences the stability of a community function is a major question in ecology. However, only limited empirical investigations of the diversity–stability relationship in soil microbial communities have been undertaken, despite the fundamental role of microbial communities in driving carbon and nutrient cycling in terrestrial ecosystems. In this study, we conducted a microcosm experiment to investigate the relationship between microbial diversity and stability of soil decomposition activities against changes in decomposition substrate quality by manipulating microbial community using selective biocides. We found that soil respiration rates and degradation enzyme activities by a coexisting fungal and bacterial community (a taxonomically diverse community) are more stable against changes in substrate quality (plant leaf materials) than those of a fungi-dominated or a bacteria-dominated community (less diverse community). Flexible changes in the microbial community composition and/or physiological state in the coexisting community against changes in substrate quality, as inferred by the soil lipid profile, may be the mechanism underlying this positive diversity–stability relationship. Our experiment demonstrated that the previously found positive diversity–stability relationship could also be valid in the soil microbial community. Our results also imply that the functional/taxonomic diversity and community ecology of soil microbes should be incorporated into the context of climate–ecosystem feedbacks. Changes in substrate quality, which could be induced by climate change, have impacts on decomposition process and carbon dioxide emission from soils, but such impacts may be attenuated by the functional diversity of soil microbial communities.     

Soil microbial responses to experimental warming and clipping in a tallgrass prairie

Global surface temperature is predicted to increase by 1.4–5.8°C by the end of this century. However, the impacts of this projected warming on soil C balance and the C budget of terrestrial ecosystems are not clear. One major source of uncertainty stems from warming effects on soil microbes, which exert a dominant influence on the net C balance of terrestrial ecosystems by controlling organic matter decomposition and plant nutrient availability. We, therefore, conducted an experiment in a tallgrass prairie ecosystem at the Great Plain Apiaries (near Norman, OK) to study soil microbial responses to temperature elevation of about 2°C through artificial heating in clipped and unclipped field plots. While warming did not induce significant changes in net N mineralization, soil microbial biomass and respiration rate, it tended to reduce extractable inorganic N during the second and third warming years, likely through increasing plant uptake. In addition, microbial substrate utilization patterns and the profiles of microbial phospholipid fatty acids (PLFAs) showed that warming caused a shift in the soil microbial community structure in unclipped subplots, leading to the relative dominance of fungi as evidenced by the increased ratio of fungal to bacterial PLFAs. However, no warming effect on soil microbial community structure was found in clipped subplots where a similar scale of temperature increase occurred. Clipping also significantly reduced soil microbial biomass and respiration rate in both warmed and unwarmed plots. These results indicated that warming‐led enhancement of plant growth rather than the temperature increase itself may primarily regulate soil microbial response. Our observations show that warming may increase the relative contribution of fungi to the soil microbial community, suggesting that shifts in the microbial community structure may constitute a major mechanism underlying warming acclimatization of soil respiration.     

Soil acidification mediates changes in soil bacterial community assembly processes in response to agricultural intensification

Agricultural intensification is known to alter the assembly of soil microbial communities, which regulate several critical ecosystem processes. However, the underlying ecological processes driving changes in microbial community assembly, particularly at the regional scale, remain poorly understood. Using 16S rDNA sequencing, we characterized soil bacterial community assembly in three land-use types with increasing land-use intensity: open fields cultivated with main crops (CF) or vegetables (VF), and greenhouses cultivated with vegetables (VG). Compared with CF, VF and VG altered bacterial community composition and decreased spatial turnover rates of edaphic variables and bacterial communities. Bacterial community assembly was primarily governed by deterministic processes; however, bacterial communities in VF and VG were phylogenetically less clustered and more influenced by variable selection and less by dispersal limitation. Soil pH was the most important edaphic variable mediating the changes in bacterial community assembly processes induced by agricultural intensification. Specifically, decreasing soil pH led to stochastic assembly of bacterial community. Soil pH was lower in more intensively managed lands, especially in case of VG (pH range: 5.86–7.42). Overall, agricultural intensification altered soil bacterial community assembly processes, which was associated with soil acidification. These findings may have implications for improving soil quality and agroecosystem sustainability.     

Microbial communities are indicators of parasite infection status

Growing evidence suggests that microbiomes have been shaping the evolutionary pathways of macroorganisms for millennia and that these tiny symbionts can influence, and possibly even control, species interactions like host–parasite relationships. Yet, while studies have investigated host–parasites and microbiomes separately, little has been done to understand all three groups synergistically. Here, we collected infected and uninfected Eurypanopeus depressus crab hosts from a coastal North Carolina oyster reef three times over 4 months. Infected crabs demonstrated an external stage of the rhizocephalan parasite, Loxothylacus panopaei. Community analyses revealed that microbial richness and diversity were significantly different among tissue types (uninfected crab, infected crab, parasite externae and parasite larvae) and over time (summer and fall). Specifically, the microbial communities from parasite externae and larvae had similar microbiomes that were consistent through time. Infected crabs demonstrated microbial communities spanning those of their host and parasite, while uninfected crabs showed more distinctive communities with greater variability over time. Microbial communities were also found to be indicators of early-stage infections. Resolving the microbial community composition of a host and its parasite is an important step in understanding the microbiome's role in the host–parasite relationship and determining how this tripartite relationship impacts coevolutionary processes.     

全球变暖背景下土壤微生物呼吸的热适应性:证据、机理和争议

土壤微生物呼吸的热适应性被认为是决定陆地生态系统对全球变暖反馈作用的潜在重要机制,可能显著改变未来的气候变化趋势,然而学术界对于这一机制是否真实存在尚有分歧。阐述了土壤微生物呼吸的热适应性概念,从证据、机理和争议3方面对已有研究进展进行了综述和分析。土壤微生物呼吸的热适应性是微生物在群落尺度上对温度变化的适应性,具有坚实的生物学与生态学理论基础,研究者们运用各类指标已在许多实验中证实土壤微生物物种及群落的呼吸过程能够在高温环境产生适应性变化。土壤微生物呼吸的热适应性机理涉及生物膜结构变化、酶活性变化、微生物碳分配比例变化和微生物群落结构变化等方面。关于土壤微生物呼吸热适应性的争议可能是由研究方法、微生物物种及环境条件的差异引起的。根据对已有研究的分析,认为土壤微生物呼吸的热适应性是真实存在的,未来的研究可进一步探索土壤微生物呼吸的热适应性机理,深入研究环境和全球变化对土壤微生物呼吸的热适应性影响,定量评估土壤微生物呼吸的热适应性对陆地生态系统反馈过程的影响。     

干湿交替下草地生态系统土壤呼吸变化的微生物响应机制研究进展

草地是陆地生态系统中最重要、分布最广的生态系统类型之一,对全球碳循环和气候调节有着重要的作用和效应.我国拥有极为丰富的草地资源,是巨大的陆地碳储存库,也是全球碳循环重要组成部分.干湿交替是土壤中普遍发生的自然现象,这种现象的发生可能会加速土壤的碳矿化过程、激增土壤呼吸以及影响微生物的活性和群落结构等.在全球变化日趋显著的背景下,降雨量、降雨强度以及降雨频率的变化将会加速土壤干湿交替进程,进而带来微生物活性、群落结构以及土壤呼吸的变化,并对全球碳循环过程产生重要影响.本文综述了近十年来国内外的相关文献,对干湿交替条件下,土壤释放CO₂消耗碳源、土壤呼吸随时间的动态变化趋势以及土壤呼吸与微生物量、微生物活性和微生物群落结构之间的关系进行了分析和总结,以期为更好地理解干湿交替过程中草地生态系统土壤呼吸的微生物学响应机制,更准确地预测和评估未来的全球陆地生态系统的碳收支与气候变化提供一定的理论基础.