[show abstract][hide abstract] ABSTRACT: High-throughput sequencing technologies are now allowing us to study patterns of community assembly for diverse microbial assemblages across environmental gradients and during succession. Here we discuss potential explanations for similarities and differences in bacterial and fungal community assembly patterns along a soil chronosequence in the foreland of a receding glacier. Although the data are not entirely conclusive, they do indicate that successional trajectories for bacteria and fungi may be quite different. Recent empirical and theoretical studies indicate that smaller microbes (like most bacteria) are less likely to be dispersal limited than are larger microbes – which could result in a more deterministic community assembly pattern for bacteria during primary succession. Many bacteria are also better adapted (than are fungi) to life in barren, early-successional sediments in that some can fix nitrogen and carbon from the atmosphere – traits not possessed by any fungi. Other differences between bacteria and fungi are discussed, but it is apparent from this and other recent studies of microbial succession that we are a long way from understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession. We especially need a better understanding of global and regional patterns of microbial dispersal and what environmental factors control the development of microbial communities in complex natural systems.
[show abstract][hide abstract] ABSTRACT: Despite the central role of microorganisms in biogeochemistry, process models rarely explicitly account for variation in communities. Here, we use statistical models to address a fundamental question in ecosystem ecology: do we need to better understand microbial communities to accurately predict ecosystem function? Nitrogen (N) cycle process rates and associated gene abundances were measured in tropical rainforest soil samples collected in May (early wet season) and October (late wet season). We used stepwise linear regressions to examine the explanatory power of edaphic factors and functional gene relative abundances alone and in combination for N-cycle processes, using both our full dataset and seasonal subsets of the data. In our full dataset, no models using gene abundance data explained more variation in process rates than models based on edaphic factors alone, and models that contained both edaphic factors and community data did not explain significantly more variation in process rates than edaphic factor models. However, when seasonal datasets were examined separately, microbial predictors enhanced the explanatory power of edaphic predictors on dissimilatory nitrate reduction to ammonium and N2O efflux rates during October. Because there was little variation in the explanatory power of microbial predictors alone between seasonal datasets, our results suggest that environmental factors we did not measure may be more important in structuring communities and regulating processes in October than in May. Thus, temporal dynamics are key to understanding the relationships between edaphic factors, microbial communities and ecosystem function in this system. The simple statistical method presented here can accommodate a variety of data types and should help prioritize what forms of data may be most useful in ecosystem model development.
Soil Biology and Biochemistry 01/2014; 68:279–282. · 3.65 Impact Factor
[show abstract][hide abstract] ABSTRACT: The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in response to increasing atmospheric CO2 concentrations or atmospheric nutrient deposition.
[show abstract][hide abstract] ABSTRACT: Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be impor- tant for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.
[show abstract][hide abstract] ABSTRACT: SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.
[show abstract][hide abstract] ABSTRACT: Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.
[show abstract][hide abstract] ABSTRACT: Background: Photosynthetic crust communities are important to the functioning of many desert and early successional ecosystems. Little is known about the factors that limit the growth of these communities, especially during early stages of primary succession or following disturbance.
Aims: Our main goal was to develop a method to study nutrient limitations of crust growth in laboratory microcosms. We used the new method to test the hypothesis that phosphorus limits the growth of crusts in newly deglaciated soils of the high Andes. Methods: We modified the point–intercept method used in plant ecology to quantify the spread of cyanobacteria, algae and mosses on the soil surface in response to additions of nitrogen and phosphorus.
Results: Fertilization with phosphorus significantly increased the growth rate and final percentage cover, and decreased the lag time for growth of cyanobacterial and algal communities in recently deglaciated soils. By contrast, nitrogen additions had no significant effect on the growth of microbial phototrophs, and all nutrient additions suppressed the growth of early successional mosses.
Conclusions: We propose that the method described here offers a valuable tool for assessing the nature of nutrient limitation of photosynthetic organisms in early successional and desert ecosystems. The information provided by using this approach can increase our understanding of the earliest stages of ecosystem development and may help inform strategies for the reclamation of disturbed arid ecosystems by identifying potential limiting nutrients.
[show abstract][hide abstract] ABSTRACT: Global changes such as variations in plant net primary production are likely to drive shifts in leaf litterfall inputs to forest soils, but the effects of such changes on soil carbon (C) cycling and storage remain largely unknown, especially in C-rich tropical forest ecosystems. We initiated a leaf litterfall manipulation experiment in a tropical rain forest in Costa Rica to test the sensitivity of surface soil C pools and fluxes to different litter inputs. After only 2 years of treatment, doubling litterfall inputs increased surface soil C concentrations by 31%, removing litter from the forest floor drove a 26% reduction over the same time period, and these changes in soil C concentrations were associated with variations in dissolved organic matter fluxes, fine root biomass, microbial biomass, soil moisture, and nutrient fluxes. However, the litter manipulations had only small effects on soil organic C (SOC) chemistry, suggesting that changes in C cycling, nutrient cycling, and microbial processes in response to litter manipulation reflect shifts in the quantity rather than quality of SOC. The manipulation also affected soil CO 2 fluxes; the relative decline in CO 2 production was greater in the litter removal plots (-22%) than the increase in the litter addition plots (+15%). Our analysis showed that variations in CO 2 fluxes were strongly correlated with microbial biomass pools, soil C and nitrogen (N) pools, soil inorganic P fluxes, dissolved organic C fluxes, and fine root biomass. Together, our data suggest that shifts in leaf litter inputs in response to localized human disturbances and global environmental change could have rapid and important consequences for belowground C storage and fluxes in tropical rain forests, and highlight differences between tropical and temperate ecosystems, where belowground C cycling responses to changes in litterfall are generally slower and more subtle.
Global Change Biology 09/2012; 18(9):2969-79. · 6.91 Impact Factor
[show abstract][hide abstract] ABSTRACT: Soil microorganisms are key drivers of terrestrial biogeochemical cycles, yet it is still unclear how variations in soil microbial community composi-tion influence many ecosystem processes. We investigated how shifts in bacterial community composition and diversity resulting from differ-ences in carbon (C) availability affect organic matter decomposition by conducting an in situ litter manipulation experiment in a tropical rain forest in Costa Rica. We used bar-coded pyrose-quencing to characterize soil bacterial community composition in litter manipulation plots and per-formed a series of laboratory incubations to test the potential functional significance of community
[show abstract][hide abstract] ABSTRACT: In the McMurdo Dry Valleys of Antarctica, stream biota is limited by the brief availability of liquid water. The benthic microbial mats harbor diatoms that have adapted to hydrologic stresses, including numerous endemic species. We found a strong relationship between diatom community composition and flow intermittency in a data set including seven streams that spanned a gradient in flow intermittency. In particular, two genera represented by numerous endemic species in Dry Valley habitats, Hantzschia and Luticola, had high abundances in moderately and highly intermittent streams, respec-tively. The Shannon Index of diversity was greatest in streams with intermediate flow intermittency, with lower diversity in more stable streams resulting from lower evenness, and lower diversity in highly intermittent streams resulting from lower richness. These results indicate that multiple metrics of biodiversity may be useful in assessing the response of diatom com-munities to changing hydrologic regime. We propose that flow intermittency acts as a species filter that increases habitat heterogeneity in Dry Valley streams and may allow endemic species to persist. Future Antarctic warming may alter diatom community composition and habitats that act as refugia for desiccation-tolerant taxa.
Résumé : Dans les vallées sèches de McMurdo de l'Antarctique, les organismes des cours d'eau sont limités par la courte disponibilité d'eau liquide. Les tapis microbiens benthiques contiennent des diatomées, dont de nombreuses espèces endémi-ques, qui se sont adaptées aux stress hydrologiques. Il existe une forte relation entre la composition de la communauté de diatomées et l'intermittence du débit dans un ensemble de données qui inclut sept cours d'eau qui couvrent un gradient de discontinuité du débit. En particulier, deux genres qui contiennent de nombreuses espèces endémiques dans les habitats des vallées sèches, Hantzschia et Luticola, atteignent de fortes abondances, respectivement dans les cours d'eau moyennement et fortement intermittents. L'indice de diversité de Shannon est maximal dans les cours d'eau qui ont un débit modérément discontinu; la diversité est plus basse dans les cours d'eau plus stables à cause d'une équitabilité plus faible et aussi plus basse dans les cours d'eau fortement intermittents à cause d'une richesse réduite. Ces résultats indiquent que l'utilisation de plusieurs métriques de la biodiversité peuvent être utiles pour évaluer la réaction des communautés de diatomées aux chan-gements de régime hydrologique. Nous croyons que la discontinuité du débit sert de filtre des espèces, augmente l'hétérogé-néité des habitats dans les cours d'eau des vallées sèches et peut permettre aux espèces endémiques de survivre. Un réchauffement futur de l'Antarctique modifiera peut-être les communautés de diatomées et les habitats qui servent de refuges pour les taxons tolérants à la dessiccation.
Canadian Journal of Fisheries and Aquatic Sciences 01/2012; 69(8):1405-1419. · 2.32 Impact Factor
[show abstract][hide abstract] ABSTRACT: Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As). This has globally important implications since As in drinking water affects the health of over 100 million people worldwide, including in the Ganges-Brahmaputra Delta region of Bangladesh where geogenic arsenic in groundwater can reach concentrations of more than 10 times the World Health Organization's limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across gradients in sediment texture and chemistry in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flow path at a range of depths between 1.5 and 15 m. We identified significant differences in bacterial community composition between locations in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C), manganese (Mn), and iron (Fe) concentrations. Deltaproteobacteria and Chloroflexi were found in higher proportions in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were in higher proportions in sandy sediments with lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance-reducers in the high C and metal sediments. It is well-documented that C, Mn, and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community.
[show abstract][hide abstract] ABSTRACT: One of the oldest ecological hypotheses, proposed by Darwin, suggests that the struggle for existence is stronger between more closely related species. Despite its long history, the validity of this phylogenetic limiting similarity hypothesis has rarely been examined. Here we provided a formal experimental test of the hypothesis using pairs of bacterivorous protist species in a multigenerational experiment. Consistent with the hypothesis, both the frequency and tempo of competitive exclusion, and the reduction in the abundance of inferior competitors, increased with increasing phylogenetic relatedness of the competing species. These results were linked to protist mouth size, a trait potentially related to resource use, exhibiting a significant phylogenetic signal. The likelihood of coexistence, however, was better predicted by phylogenetic relatedness than trait similarity of the competing species. Our results support phylogenetic relatedness as a useful predictor of the outcomes of competitive interactions in ecological communities.
[show abstract][hide abstract] ABSTRACT: Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
[show abstract][hide abstract] ABSTRACT: Estimating phosphorus (P) availability is difficult—particularly in infertile soils such as those exposed after glacial recession—because standard P extraction methods may not mimic biological acquisition pathways. We developed an approach, based on microbial CO2 production kinetics and conserved carbon:phosphorus (C:P) ratios, to estimate the amount of P available for microbial growth in soils and compared this method to traditional, operationally-defined indicators of P availability. Along a primary succession gradient in the High Andes of Perú, P additions stimulated the growth-related (logistic) kinetics of glutamate mineralization in soils that had been deglaciated from 0 to 5years suggesting that microbial growth was limited by soil P availability. We then used a logistic model to estimate the amount of C incorporated into biomass in P-limited soils, allowing us to estimate total microbial P uptake based on a conservative C:P ratio of 28:1 (mass:mass). Using this approach, we estimated that there was
[show abstract][hide abstract] ABSTRACT: Our paper describes the ecological controls on algal-mat diatom communities in the dynamic stream ecosystems of the McMurdo Dry Valleys in Antarctica. Dry Valley diatom communities are relatively diverse, and nearly ½ of the taxa found in these mats are considered endemic. Diatom community composition was examined in 5 streams in Taylor Valley during a 15-y cooling period that included a discrete flood event. Two hydrologic variables, total annual discharge and historical variation in discharge, gave the most parsimonious model of among-stream and interannual variation in diatom communities. Algal-mat biomass and chlorophyll a concentrations decreased after the flood, which occurred during the 2001/2002 summer season. Most algal-mat diatom communities recovered quickly after the flood. However, Green Creek, a relatively high-flow stream with low historical variation in discharge, appears to have experienced a persistent diatom community shift toward increased relative abundance of small, generalist species. Diatom relative biovolume, a proxy for the size of diatoms within a sample, was negatively correlated with stream flow, such that higher-discharge streams contained greater relative abundances of smaller diatoms than lower-flow streams. Therefore, diatom size may play a role in determining the distribution of a species in these streams and may be useful for monitoring environmental changes. Our study demonstrates the importance of understanding factors affecting ecosystem resilience, especially in polar regions, which are experiencing rapid climate changes. Hydrologic disturbances and flow regime lay the foundation for stream ecosystem functioning and community development (Peterson 1996, Biggs and Smith 2002). The importance of flow variability is evident in intermittent rivers, and its role in maintaining biodiversity and ecosystem health is increasingly recognized in regulated systems across the globe (Poff et al. 2007). Low-flow disturbances occur frequently in hot and cold desert streams and can desiccate stream algal mats. Few studies have examined the effects of these disturbances on diatom communities in situ. In one study, low-flow disturbance events altered long-term algal assemblages such that the mature community was better adapted to both high-and low-flow extremes (Ledger et al. 2008). Furthermore, certain desert diatoms are physiologically capable of surviving dry periods (Hostetter and Hoshaw 1970), and other diatoms may be protected by existing within desiccation-resistant biofilms or microbial mats produced by other members of the microbial community (Peterson 1987, Davey 1989). In polar environments, diatoms in algal mats appear to be influenced by hydrologic regime. For example, in the high Arctic, Antoniades et al. (2009) found that differences in diatom communities across 42 streams could not be explained by water chemistry or geography alone and postulated that a dynamic, meltwater-driven flow regime may influence diatom communities. Resilience was shown in a Canadian Arctic stream, where diatom communities quickly returned to predisturbance conditions after a high-flow event (Stewart et al. 2005).
Journal of the North American Benthological Society 01/2011; 30(4):1057-1073. · 2.96 Impact Factor
[show abstract][hide abstract] ABSTRACT: Bacteria control major nutrient cycles and directly influence plant, animal and human health. However, we know relatively little about the forces shaping their large-scale ecological ranges. Here, we reveal patterns in the distribution of individual bacterial taxa at multiple levels of phylogenetic resolution within and between Earth's major habitat types. Our analyses suggest that while macro-scale habitats structure bacterial distribution to some degree, abundant bacteria (i.e. detectable using 16S rRNA gene sequencing methods) are confined to single assemblages. Additionally, we show that the most cosmopolitan taxa are also the most abundant in individual assemblages. These results add to the growing body of data that support that the diversity of the overall bacterial metagenome is tremendous. The mechanisms governing microbial distribution remain poorly understood, but our analyses provide a framework with which to test the importance of macro-ecological environmental gradients, relative abundance, neutral processes and the ecological strategies of individual taxa in structuring microbial communities.
[show abstract][hide abstract] ABSTRACT: Arsenic contamination of groundwater is a global health crisis, especially in Bangladesh where an estimated 40 million people are at risk. The release of geogenic arsenic bound to sediments into groundwater is thought to be influenced by dissolved organic matter (DOM) through several biogeochemical processes. Abiotically, DOM can promote the release of sediment bound As through the formation of DOM-As complexes and competitive interactions between As and DOM for sorption sites on the sediment. Additionally, the labile portion of groundwater DOM can serve as an electron donor to support microbial growth and the more recalcitrant humic DOM may serve as an electron shuttle, facilitating the eventual reduction of ferric iron present as iron oxides in sediments and consequently the mobilization of sorbed As and organic material. The goal of this study is to understand the source of DOM in representative Bangladesh groundwaters and the DOM sorption processes that occur at depth. We report chemical characteristics of representative DOM from a surface water, a shallow low-As groundwater, mid-depth high-As groundwater from the Araihazar region of Bangladesh. The humic DOM from groundwater displayed a more terrestrial chemical signature, indicative of being derived from plant and soil precursor materials, while the surface water humic DOM had a more microbial signature, suggesting an anthropogenic influence. In terms of biogeochemical processes occurring in the groundwater system, there is evidence from a diverse set of chemical characteristics, ranging from 13C-NMR spectroscopy to the analysis of lignin phenols, for preferential sorption onto iron oxides influencing the chemistry and reactivity of humic DOM in high As groundwater in Bangladesh. Taken together, these results provide chemical evidence for anthropogenic influence and the importance of sorption reactions at depth controlling the water quality of high As groundwater in Bangladesh.