Modelling spatial patterns in host-associated microbial communities

Microbial communities exhibit spatial structure at different scales, due to constant interactions with their environment and dispersal limitation. While this spatial structure is often considered in studies focusing on free-living environmental communities, it has received less attention in the context of host-associated microbial communities or microbiota. The wider adoption of methods accounting for spatial variation in these communities will help to address open questions in basic microbial ecology as well as realize the full potential of microbiome-aided medicine. Here, we first overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota. We outline a number of topical open questions in the field related to spatial variation and patterns. We then review the existing methodology for the spatial modelling of microbiota. We suggest that methodology from related fields, such as systems biology and macro-organismal ecology, could be adapted to obtain more accurate models of spatial structure. We further posit that methodological developments in the spatial modelling and analysis of microbiota could in turn broadly benefit theoretical and applied ecology and contribute to the development of novel industrial and clinical applications.     

Engineering synthetic spatial patterns in microbial populations and communities

1. Download : Download high-res image (148KB)
2. Download : Download full-size image

     

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.     

Temporal and spatial variation of litter production in Sonoran Desert communities

The seasonal pattern of litter production was analyzed in three contiguous desert communities near the southern boundaries of the Sonoran Desert. There was a large spatial variation in annual litter production mainly caused by differences in the composition and structure of vegetation. In the most productive site (Arroyos) annual litterfall was 357 g m^-2yr^-1, a figure higher than some tropical deciduous forests. Litter production was only 60g m^-2yr^-1in the open desert in the plains (Plains) and 157 g m^-2yr^-1 in the thornscrub on the slopes (Hillsides). Topographic and hydrologic features influence the composition, structure and function of the vegetation, modifying the general relationship between rainfall and productivity described for desert ecosystems. The temporal pattern of litter production showed marked seasonality with two main periods of heavy litterfall: one after the summer rains from September to November (autumn litter production) and another after the winter rains from March to May (spring litter production). In the open desert areas, spring litter production was significantly higher than the autumn pulse, while in the slopes, the autumn production was the most important. The Arroyos site produced similar litterfall amounts during the two dry seasons. The species composition defined the season of maximum leaf-fall. In the Plains, the vigorous winter growth of ephemeral and perennial plants made up most of the litter production, while in the Hillsides, most perennials remained dormant throughout the winter-spring period and a significant peak of litterfall occurred only after the summer growth. This difference in growth between seasons was less pronounced in the Arroyos. The timing of maximum production of reproductive and woody litter also differed from site to site.     

Temporal dynamics of microbial communities in microcosms in response to pollutants

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n‐octadecane, phenanthrene + n‐octadecane and phenanthrene + n‐octadecane + CdCl₂). Subculturing was performed at 10‐day intervals, followed by high‐throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co‐occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re‐equilibration of microbial communities.     

Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan

The spatial and temporal variability of bacterial communities were determined for the nearshore waters of Lake Michigan, an oligotrophic freshwater inland sea. A freshwater estuary and nearshore sites were compared six times during 2006 using denaturing gradient gel electrophoresis (DGGE). Bacterial composition clustered by individual site and date rather than by depth. Seven 16S rRNA gene clone libraries were constructed, yielding 2717 bacterial sequences. Spatial variability was detected among the DGGE banding patterns and supported by clone library composition. The clone libraries from deep waters and the estuary environment revealed highest overall bacterial diversity. Betaproteobacteria sequence types were the most dominant taxa, comprising 40.2–67.7% of the clone libraries. BAL 47 was the most abundant freshwater cluster of Betaproteobacteria , indicating widespread distribution of this cluster in the nearshore waters of Lake Michigan. Incertae sedis 5 and Oxalobacteraceae sequence types were prevalent in each clone library, displaying more diversity than previously described in other freshwater environments. Among the Oxalobacteraceae sequences, a globally distributed freshwater cluster was determined. The nearshore waters of Lake Michigan are a dynamic environment that experience forces similar to the coastal ocean environment and share common bacterial diversity with other freshwater habitats.     

Temporal and spatial patterns of soil water following wildfire-induced changes in plant communities in the Great Basin in Nevada,USA

Infection of tall fescue (Festuca arundinacea Schreb.) with its endemicNeotyphodium coenophialum-endophyte (Morgan-Jones and Gams) Glenn, Bacon and Hanlin appears to reduce copper (Cu) concentrations in forage and serum of grazing animals, contributing to a range of immune-related disorders. A greenhouse experiment was conducted to identify effects of novel endophyte strains on Cu acquisition by tall fescue (Festuca arundinacea Schreb.) varieties Grasslands Flecha and Jesup infected with a novel, non ergot producing endophyte strain AR542, and two perennial ryegrass (Lolium perenne L.) varieties Aries and Quartet infected with a novel, non lolitrem B producing strain AR1, and their noninfected (E−) forms. Individual endophyte/grass associations were cultivated in nutrient solutions at 1.0 (P+) and 0.0 mM (P−) phosphorus concentrations. The Cu²⁺-binding activity of extracellular root exudates, and concentrations of Cu and other heavy metals in roots and shoots were measured. Extracellular root exudates of AR542-infected vs. E− tall fescue had higher Cu²⁺-binding activity only in P− nutrient solution as shown by lower concentration of free Cu²⁺ (0.096 vs. 0.188 mmol Cu²⁺ g⁻¹ root DM, respectively). The Cu²⁺-binding activity by root exudates of perennial ryegrass was not affected by endophyte infection, but was higher (i.e., lower concentration of free Cu²⁺) in P− vs. P+ nutrient solution (0.068 vs. 0.114 mmol Cu²⁺ g⁻¹ root DM). In this hydroponic experiment, Cu concentrations in shoots of both grasses were not a function of Cu²⁺-binding activity and endophyte effects on heavy metal concentrations in shoots and roots were specific for each variety. The Cu²⁺-binding activity of extracellular root exudates may affect Cu accumulation by field-grown, endophyte-infected tall fescue under P-limiting growth conditions and warrants verification by more specific methods.     

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities

Although elevated CO₂ (eCO₂) significantly affects the α‐diversity, composition, function, interaction and dynamics of soil microbial communities at the local scale, little is known about eCO₂ impacts on the geographic distribution of micro‐organisms regionally or globally. Here, we examined the β‐diversity of 110 soil microbial communities across six free air CO₂ enrichment (FACE) experimental sites using a high‐throughput functional gene array. The β‐diversity of soil microbial communities was significantly (P < 0.05) correlated with geographic distance under both CO₂ conditions, but declined significantly (P < 0.05) faster at eCO₂ with a slope of ?0.0250 than at ambient CO₂ (aCO₂) with a slope of ?0.0231 although it varied within each individual site, indicating that the spatial turnover rate of soil microbial communities was accelerated under eCO₂ at a larger geographic scale (e.g. regionally). Both distance and soil properties significantly (P < 0.05) contributed to the observed microbial β‐diversity. This study provides new hypotheses for further understanding their assembly mechanisms that may be especially important as global CO₂ continues to increase.     

Temporal changes in therophytic communities across the boundary of disturbed-intact ecosystems

External control processes cause continual compositional and structural readjustments of Mediterranean pasture ecosystems. Such control processes include herbivore grazing, meteorological fluctuations and traditional management activities, which determine the stable environment where the succession occurs. Traditional management in this ecosystem frequently involves periodic ploughing or controlled fires.Experimental disturbances were applied to pastures of different maturity. Recovery was studied by relating information gathered for each disturbed system to successional age. The boundary between original systems of differing ages and the newly created systems was studied to compare the space-time evolution of therophytic communities. Permanent transects perpendicular to the disturbance boundaries and containing many small plots were sampled during consecutive years.Sampling plots located on both sides of the boundaries were classified into communities, in order to detect the space-time pasture evolution in successive years. Annual conditional probabilities were calculated for transitions between the recognised communities. During succession different strategies were detected in response to meteorological variations. In pioneer successional stages, substitutions of one community by another in the same space seem to be random. However, greater determinism was detected in more mature pastures, where, in addition, communities' abundance does not respond to meteorological change.Nomenclature follows T. G. Tutin et al. 1964–1980. Flora Europaea. Cambridge University Press, Cambridge.     

Temporal and spatial patterns of eukaryotic and bacterial communities found in vernal pools

In this study, we examined the effects of physicochemical variability on the microbial communities of vernal pools. Denaturing gradient gel electrophoresis revealed temporal changes to be more pronounced than spatial changes in eukaryotic and bacterial communities. Sequencing revealed high degrees of richness in decomposers, which supports the notion that vernal pools are heterotrophic habitats.     

三江平原北部生态系统服务价值的时空演变

以三江平原北部地区2市5县为研究区,采用生态系统服务价值评估方法对1954—2009年间三江平原北部地区生态系统服务价值进行估算,以期全面分析土地生态系统服务价值随时空变化的特点。结果表明:(1)1954—2009年间三江平原北部地区的不同土地利用类型面积变化显著,农田变化速度最快,其次为湿地,人口数量的增加及保证粮食增产是土地利用变化的主要驱动力。(2)1954—2009年三江平原北部地区生态系统服务价值总量逐渐减少,共减少779.51亿元。长期的土地垦殖是三江平原北部地区生态系统服务价值减少的主要驱动因素。(3)就各土地利用类型生态系统服务价值而言,55年间除农田生态系统和水域生态系统生态服务价值是增加外,其余各生态系统服务价值均在减少。湿地生态系统服务价值减少值最大,其次为林地生态系统服务价值。各项生态系统服务功能除与农田相关的食物生产在增加,其余也均呈减少趋势。(4)不同地区单位面积生态系统服务价值损失量也不相同,湿地、林地面积比重下降幅度大、且农田面积比重上升幅度大的区域,其单位面积生态系统服务价值损失量也较大。     

Seasonal and spatial diversity of microbial communities in marine sediments of the South China Sea

This study was conducted to characterize the diversity of microbial communities in marine sediments of the South China Sea by means of 16S rRNA gene clone libraries. The results revealed that the sediment samples collected in summer harboured a more diverse microbial community than that collected in winter, Deltaproteobacteria dominated 16S rRNA gene clone libraries from both seasons, followed by Gammaproteobacteria, Acidobacteria, Nitrospirae, Planctomycetes, Firmicutes. Archaea phylotypes were also found. The majority of clone sequences shared greatest similarity to uncultured organisms, mainly from hydrothermal sediments and cold seep sediments. In addition, the sedimentary microbial communities in the coastal sea appears to be much more diverse than that of the open sea. A spatial pattern in the sediment samples was observed that the sediment samples collected from the coastal sea and the open sea clustered separately, a novel microbial community dominated the open sea. The data indicate that changes in environmental conditions are accompanied by significant variations in diversity of microbial communities at the South China Sea.     

Temporal changes of local and regional processes in the assembly of herbivorous insect communities

Herbivorous insect communities are structured by multiple processes operating locally (e.g. bottom–up effects of plants) and regionally (e.g. dispersal limitation). Although the relative strength of these processes has been well documented, how it varies in time is less understood, especially in relation with the temporal dynamics of plant communities. If temporal turnover of local plant species composition is too rapid for insect community assembly to keep up with, bottom–up effects are expected to be weak. Here, in plant and herbivorous insect communities in Japanese grasslands, we studied how the relative importance of local (bottom–up effects of plants, structures of plant communities and top–down effects of predators) and regional (dispersal limitation) processes varies over the growing season. In addition, we tested the hypothesis that larger temporal turnover of plant species composition is related to the weaker bottom–up effects, that is, the lower explanation power of plant communities for insect communities. We found that, throughout the growing season, the insect species composition was mainly explained by local variables (plant species composition, vegetation height and predator abundance), and their explanation power was higher during later phases of the season (late summer). Furthermore, the variation not explained by plant species composition was correlated with the degree of temporal turnover of plants, suggesting that insect communities failed to track the temporal turnover of plant species. These results were pronounced when we focused on leaf sucker insects, whose host plant range is presumably more limited. We conclude that herbivorous insect communities are mainly regulated by local processes, especially bottom–up effects from plants, while stochasticity may have played a role in early phases of the season. Furthermore, we underscore the importance of considering relative time scale of community assembly and environmental shifts, especially in systems characterized by dynamic changes.     

Temporal and spatial changes in a mountainous area of central Italy

Abstract. In this paper we present an application of aerial remote sensing to the analysis of spatial information in a mountainous area of central Italy by applying texture measures and landscape indices. Land cover data acquired in different time periods are used to calculate measures of landscape pattern and structure at pixel level (tone and texture variables) and patch‐level (landscape indices). Images of the patches from the 1950s, 1980s and 1990s have been derived from the tone‐texture classification of scanned black‐and‐white photographs. Multitemporal analysis of landscape indices has been performed to detect changes of landscape elements and related effects on vegetation dynamics due to the reduction of human impact.     

Resistance and resilience of microbial communities - temporal and spatial insurance against perturbations

Bacteria play fundamental roles for many ecosystem processes; however, little empirical evidence is available on how environmental perturbations affect their composition and function. We investigated how spatial and temporal refuges affect the resistance and resilience of a freshwater bacterioplankton community upon a salinity pulse perturbation in continuous cultures. Attachment to a surface avoided the flushing out of cells and enabled re-colonization of the liquid phase after the perturbation, hence serving as a temporal refuge. A spatial refuge was established by introduction of bacteria from an undisturbed reservoir upstream of the continuous culture vessel, acting analogous to a regional species pool in a metacommunity. The salinity pulse affected bacterial community composition and the rates of respiration and the pattern of potential substrate utilization as well as the correlation between composition and function. Compared with the no-refuge treatment, the temporal refuge shortened return to pre-perturbation conditions, indicating enhanced community resilience. Composition and function were less disturbed in the treatment providing a spatial refuge, suggesting higher resistance. Our results highlight that spatial and temporal dynamics in general and refuges in particular need to be considered for conceptual progress in how microbial metacommunities are shaped by perturbations.     

Comparison of microbial communities in four different composting processes as evaluated by denaturing gradient gel electrophoresis analysis

AIMS: We aimed to systematically understand the composting processes by a comparison of microbial communities during four full-scale composting processes. METHODS AND RESULTS: Microbial communities during the four different full-scale composting processes were analysed by denaturing gradient gel electrophoresis combined with measurement of physicochemical parameters. Two composting processes utilized sewage sludge and two utilized food-waste. Comparison of the four processes indicated that the concentration of dissolved organic carbon was higher in the food-waste-composting than in the sewage-sludge-composting processes, and microbial communities varied with composting substrate. The tendency for different microbes to appear in the composting process with different concentrations of dissolved organic carbon agreed with a previous study that showed that microbial succession occurred with a decrease in dissolved organic carbon in a laboratory-scale food-waste-composting process. CONCLUSIONS: Our results suggested that the main factor affecting microbial communities in the composting process is the concentration of dissolved organic materials. SIGNIFICANCE AND IMPACT OF THE STUDY: In addition to studying microbial communities involved in composting, this research is also the first to study composting mechanisms using molecular methods. The results of our studies may be helpful in the design and management of composting processes.