Microbial diversity–productivity relationships in aquatic ecosystems

Ecological effects on gut bacterial communities in wild bumblebee colonies

1. Animal hosts harbour diverse and often specific bacterial communities (microbiota) in their gut. These microbiota can provide crucial services to the host such as aiding in digestion of food and immune defence. However, the ecological factors correlating with and eventually shaping these microbiota under natural conditions are poorly understood. 2. Bumblebees have recently been shown to possess simple and highly specific microbiota. We here examine the dynamics of these microbiota in field colonies of the bumblebee Bombus terrestris over one season. The gut bacteria were assessed with culture-independent methods, that is, with terminal restriction fragment length profiles of the 16S rRNA gene. 3. To further understand the factors that affect the microbiota, we experimentally manipulated field-placed colonies in a fully factorial experiment by providing additional food or by priming the workers' immune system by injecting heat-killed bacteria. We furthermore looked at possible correlates of diversity and composition of the microbiota for (i) natural infections with the microbial parasites Crithidia bombi and Nosema bombi, (ii) bumblebee worker size, (iii) colony identity, and (iv) colony age. 4. We found an increase in diversity of the microbiota in individuals naturally infected with either C. bombi or N. bombi. Crithidia bombi infections, however, appear to be only indirectly linked with higher microbial diversity when comparing colonies. The treatments of priming the immune system with heat-killed bacteria and additional food supply, as well as host body size, had no effect on the diversity or composition of the microbiota. Host colony identity had only a weak effect on the composition of the microbiota at the level of resolution of our method. We found both significant increases and decreases in the relative abundance of selected bacterial taxa over the season. 5. We present the first study on the ecological dynamics of gut microbiota in bumblebees and identify parasite infections, colony identity and colony age as important factors influencing the diversity and composition of the bacterial communities. The absence of an effect of our otherwise effective experimental treatments suggests a remarkable ability of the host to maintain a homoeostasis in this community under widely different environments.

Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets

Metagenomics holds the promise of greatly advancing the study of diversity in natural communities, but novel theoretical and methodological approaches must first be developed and adjusted for these data sets. We evaluated widely used macroecological metrics of taxonomic diversity on a simulated set of metagenomic samples, using phylogenetically meaningful protein-coding genes as ecological proxies. To our knowledge, this is the first approach of this kind to evaluate taxonomic diversity metrics derived from metagenomic data sets. We demonstrate that abundance matrices derived from protein-coding marker genes reproduce more faithfully the structure of the original community than those derived from SSU-rRNA gene. We also found that the most commonly used diversity metrics are biased estimators of community structure and differ significantly from their corresponding real parameters and that these biases are most likely caused by insufficient sampling and differences in community phylogenetic composition. Our results suggest that the ranking of samples using multidimensional metrics makes a good qualitative alternative for contrasting community structure and that these comparisons can be greatly improved with the incorporation of metrics for both community structure and phylogenetic diversity. These findings will help to achieve a standardized framework for community diversity comparisons derived from metagenomic data sets.

Comparison of the cytotoxic responses of Escherichia coli (E. coli) AMC 198 to different fullerene suspensions (nC60)

Fullerenes are set to be produced on an industrial scale in anticipation of their wide applications. This calls for research on their environmental and health impacts. This study investigates and compares the cell toxicity of different aqueous fullerene aggregates. Popular C(60) dispersal methods were used to prepare four types of nC(60) aggregates. These aggregates were tested against the indicator species Escherichia coli (E. coli) AMC 198. With aggregates of around 150 nm in diameter, the THF/nC(60) suspension was very toxic and gave rise to a half maximal effective concentration (EC(50)) of 0.54 mg L(-1) in E. coli. By contrast, the Tol/nC(60) suspension exhibited a cytoprotective role while the Aqu-N(2)/nC(60) and Aqu-O(2)/nC(60) suspensions enhanced the metabolism of E. coli. Although some toxicants, such as THF and THF-peroxide, were introduced into the THF/nC(60) suspension during the dispersion, the toxicity of nC(60) itself cannot be neglected.

Community analysis of high- and low-nucleic acid-containing bacteria in NW Mediterranean coastal waters using 16S rDNA pyrosequencing

The ecological significance of the marine bacterial populations distinguishable by flow cytometry on the basis of the fluorescence (FL) of their nucleic acid (NA) content and proxies of cell size (such as side scatter, SSC) remains largely unknown. Some studies have suggested that cells with high NA (HNA) content and high SSC (HS) represent the active members of the community, while the low NA (LNA) cells are inactive members of the same phylogenetic groups. But group-specific activity measurements and phylogenetic assignment after cell sorting have suggested this is not be the case, particularly in open-ocean communities. To test the extent to which the different NA subgroups are similar, and consequently the extent to which they likely have similar ecological and biogeochemical roles in the environment, we analysed the phylogenetic composition of three populations after cell sorting [high NA-high SC (HNA-HS), high NA-low SC (HNA-LS), low NA (LNA)] by 454 pyrosequencing in two contrasting periods of the year in NW Mediterranean coastal waters (BBMO, Blanes Bay Microbial Observatory) where these three populations have recurrent seasonal patterns. Statistical analyses showed that summer and winter samples were significantly different and, importantly, the sorted populations within a sample were composed of different taxa. The majority of taxa were associated with one NA fraction only, and the degree of overlap (i.e. OTUs present simultaneously in 2 fractions) between HNA and LNA and between summer and winter communities was very small. Rhodobacterales, SAR116 and Bacteroidetes contributed primarily to the HNA fraction, whereas other groups such as SAR11 and SAR86 contributed largely to the LNA fractions. Gammaproteobacteria other than SAR86 showed less preference for one particular NA fraction. An increase in diversity was observed from the LNA to the HNA-HS fraction for both sample dates. Our results suggest that, in Blanes Bay, flow cytometric signatures of natural communities track their phylogenetic composition.

Macroecology of unicellular organisms - patterns and processes

Macroecology examines the relationship between organisms and their environment at large spatial (and temporal) scales. Typically, macroecologists explain the large-scale patterns of abundance, distribution and diversity. Despite the difficulties in sampling and characterizing microbial diversity, macroecologists have recently also been interested in unicellular organisms. Here, I review the current advances made in microbial macroecology, as well as discuss related ecosystem functions. Overall, it seems that microorganisms suit surprisingly well to known species abundance distributions and show positive relationship between distribution and adundance. Microbial species-area and distance-decay relationships tend to be weaker than for macroorganisms, but nonetheless significant. Few findings on altitudinal gradients in unicellular taxa seem to differ greatly from corresponding findings for larger taxa, whereas latitudinal gradients among microorganisms have either been clearly evident or absent depending on the context. Literature also strongly emphasizes the role of spatial scale for the patterns of diversity and suggests that patterns are affected by species traits as well as ecosystem characteristics. Finally, I discuss the large role of local biotic and abiotic variables driving the community assembly in unicellular taxa and eventually dictating how multiple ecosystem processes are performed. Present review highlights the fact that most microorganisms may not differ fundamentally from larger taxa in their large-scale distribution patterns. Yet, review also shows that many aspects of microbial macroecology are still relatively poorly understood and specific patterns depend on focal taxa and ecosystem concerned.

Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships

A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine the bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22,669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species-area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few 'laws' in ecology.

The energy-diversity relationship of complex bacterial communities in Arctic deep-sea sediments

The availability of nutrients and energy is a main driver of biodiversity for plant and animal communities in terrestrial and marine ecosystems, but we are only beginning to understand whether and how energy–diversity relationships may be extended to complex natural bacterial communities. Here, we analyzed the link between phytodetritus input, diversity and activity of bacterial communities of the Siberian continental margin (37–3427 m water depth). Community structure and functions, such as enzymatic activity, oxygen consumption and carbon remineralization rates, were highly related to each other, and with energy availability. Bacterial richness substantially increased with increasing sediment pigment content, suggesting a positive energy–diversity relationship in oligotrophic regions. Richness leveled off, forming a plateau, when mesotrophic sites were included, suggesting that bacterial communities and other benthic fauna may be structured by similar mechanisms. Dominant bacterial taxa showed strong positive or negative relationships with phytodetritus input and allowed us to identify candidate bioindicator taxa. Contrasting responses of individual taxa to changes in phytodetritus input also suggest varying ecological strategies among bacterial groups along the energy gradient. Our results imply that environmental changes affecting primary productivity and particle export from the surface ocean will not only affect bacterial community structure but also bacterial functions in Arctic deep-sea sediment, and that sediment bacterial communities can record shifts in the whole ocean ecosystem functioning.

Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton

Marine bacterioplankton studies over the annual cycle in polar systems are limited due to logistic constraints in site access and support. Here, we conducted a comparative study of marine bacterioplankton sampled at several time points over the annual cycle (12 occasions each) at sub-Antarctic Kerguelen Islands (KI) and Antarctic Peninsula (AP) coastal sites in order to establish a better understanding of the extent and nature of variation in diversity and community structure at these different latitudes (49-64S). Molecular methods targeting the 16S rRNA gene (DGGE, CE-SSCP and tag pyrosequencing) suggest a strong seasonal pattern with higher richness in winter and a clear influence of phytoplankton bloom events on bacterioplankton community structure and diversity in both locations. The distribution of sequence tags within Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the two regions. At both sites, several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed intense seasonal variation often with similar trends at both sites. This enhanced understanding of variability in dominant groups of bacterioplankton over the annual cycle contributes to an expanding baseline to understand climate change impacts in the coastal zone of polar oceans and provides a foundation for comparison with open ocean polar systems.

Productivity-diversity relationships in lake plankton communities

One of the most intriguing environmental gradients connected with variation in diversity is ecosystem productivity. The role of diversity in ecosystems is pivotal, because species richness can be both a cause and a consequence of primary production. However, the mechanisms behind the varying productivity-diversity relationships (PDR) remain poorly understood. Moreover, large-scale studies on PDR across taxa are urgently needed. Here, we examined the relationships between resource supply and phyto-, bacterio-, and zooplankton richness in 100 small boreal lakes. We studied the PDR locally within the drainage systems and regionally across the systems. Second, we studied the relationships between resource availability, species richness, biomass and resource ratio (N:P) in phytoplankton communities using Structural Equation Modeling (SEM) for testing the multivariate hypothesis of PDR. At the local scale, the PDR showed variable patterns ranging from positive linear and unimodal to negative linear relationships for all planktonic groups. At the regional scale, PDRs were significantly linear and positive for phyto- and zooplankton. Phytoplankton richness and the amount of chlorophyll a showed a positive linear relationship indicating that communities consisting of higher number of species were able to produce higher levels of biomass. According to the SEM, phytoplankton biomass was largely related to resource availability, yet there was a pathway via community richness. Finally, we found that species richness at all trophic levels was correlated with several environmental factors, and was also related to richness at the other trophic levels. This study showed that the PDRs in freshwaters show scale-dependency. We also documented that the PDR complies with the multivariate model showing that plant biomass is not mirroring merely the resource availability, but is also influenced by richness. This highlights the need for conserving diversity in order to maintain ecosystem processes in freshwaters.

Isolation and bioaugmentation of an estradiol-degrading bacterium and its integration into a mature biofilm

Bioaugmentation can alter the potential activity as well as the composition of the naturally occurring microbial biota during bioremediation of a contaminated site. The focus of the current study is the pollutant 17β-estradiol (E2), which can cause endocrine effects and is potentially harmful to aquatic biota and to public health. The community composition and function of biofilms, originating from a wetland system, as affected by augmentation of an estradiol-degrading bacterium (EDB-LI1) under different conditions, were investigated. EDB-LI1 inoculation into biofilm from two wetland ponds representing early and advanced water treatment stages, respectively, yielded three significant observations, as follows: (i) EDB-LI1, enriched from a biofilm of a constructed wetland wastewater treatment system, was detected (by quantitative PCR [qPCR] analysis) in this environment in the augmented biofilm only; (ii) the augmented biofilm acquired the ability to remove estradiol; and (iii) the bacterial community composition (analyzed by PCR-denaturing gradient gel electrophoresis [DGGE]) of the augmented biofilm differed from that of the control biofilm. Furthermore, EDB-LI1 bioaugmentation showed a higher level of removal of estradiol with biofilms that originated from the advanced-treatment-stage wetland pond than those from the early-treatment-stage pond. Hence, the bioaugmentation efficiency of EDB-LI1 depends on both the quality of the feed water and the microbial community composition in the pond.

The Humpbacked Species Richness-Curve: A Contingent Rule for Community Ecology

Functional relationships involving species richness may be unimodal, monotonically increasing, monotonically decreasing, bimodal, multimodal, U-shaped, or with no discernable pattern. The unimodal relationships are the most interesting because they suggest dynamic, nonequilibrium community processes. For that reason, they are also contentious. In this paper, we provide a wide-ranging review of the literature on unimodal (humpbacked) species richness-relationships. Though not as widespread as previously thought, unimodal patterns of species richness are often associated with disturbance, predation and herbivory, productivity, spatial heterogeneity, environmental gradients, time, and latitude. These unimodal patterns are contingent on organism and environment; we examine unimodal species richness-curves involving plants, invertebrates, vertebrates, plankton, and microbes in marine, lacustrine, and terrestrial habitats. A goal of future research is to understand the contingent patterns and the complex, interacting processes that generate them.

Wetland response to sedimentation and nitrogen loading: diversification and inhibition of nitrogen-fixing microbes

Anthropogenic inputs of nutrients and sediment simultaneously impact coastal ecosystems, such as wetlands, especially during storms. Independent and combined effects of sediment and ammonium nitrate loading on nitrogen fixation rates and diversity of microbes that fix nitrogen (diazotrophs) were tested via field manipulations in Spartina foliosa and unvegetated zones at Tijuana Estuary (California, USA). This estuary is subject to episodic nitrogen enrichment and sedimentation associated with rain-driven flooding and slope instabilities, the latter of which may worsen as the Triple Border Fence is constructed along the U.S.-Mexico border. Responses of diazotrophs were assessed over 17 days using acetylene reduction assays and genetic fingerprinting (terminal restriction fragment length polymorphism [T-RFLP]) of nifH, which codes for dinitrogenase reductase. Sulfate-reducing bacteria performed approximately 70% of nitrogen fixation in Spartina foliosa rhizospheres in the absence of nitrogen loading, based on sodium molybdate inhibitions in the laboratory. Following nutrient additions, richness (number of T-RFs [terminal restriction fragments]) and evenness (relative T-RF fluorescence) of diazotrophs in surface sediments increased, but nitrogen fixation rates decreased significantly within 17 days. These responses illustrate, within a microbial community, conformance to a more general ecological pattern of high function among assemblages of low diversity. Diazotroph community composition (T-RF profiles) and rhizosphere diversity were not affected. Pore water ammonium concentrations were higher and more persistent for 17 days in plots receiving sediment additions (1 cm deep), suggesting that recovery of diazotroph functions may be delayed by the combination of sediment and nutrient inputs. Nitrogen fixation constitutes a mechanism for rapid transfer of fixed N to S. foliosa roots and a variety of primary consumers (within 3 and 8 days, respectively), as determined via 15N2 enrichment studies with in situ microcosms of intact marsh sediment. Thus, long-term declines in nitrogen fixation rates in response to increasingly frequent nutrient loading and sedimentation may potentially alter nitrogen sources for vascular plants as well as trophic pathways in wetland ecosystems.

A global network of coexisting microbes from environmental and whole-genome sequence data

Microbes are the most abundant and diverse organisms on Earth. In contrast to macroscopic organisms, their environmental preferences and ecological interdependencies remain difficult to assess, requiring laborious molecular surveys at diverse sampling sites. Here, we present a global meta-analysis of previously sampled microbial lineages in the environment. We grouped publicly available 16S ribosomal RNA sequences into operational taxonomic units at various levels of resolution and systematically searched these for co-occurrence across environments. Naturally occurring microbes, indeed, exhibited numerous, significant interlineage associations. These ranged from relatively specific groupings encompassing only a few lineages, to larger assemblages of microbes with shared habitat preferences. Many of the coexisting lineages were phylogenetically closely related, but a significant number of distant associations were observed as well. The increased availability of completely sequenced genomes allowed us, for the first time, to search for genomic correlates of such ecological associations. Genomes from coexisting microbes tended to be more similar than expected by chance, both with respect to pathway content and genome size, and outliers from these trends are discussed. We hypothesize that groupings of lineages are often ancient, and that they may have significantly impacted on genome evolution.

Dispersal scales up the biodiversity-productivity relationship in an experimental source-sink metacommunity

The influence of biodiversity on ecosystem functioning is a major concern of ecological research. However, the biodiversity-ecosystem functioning relationship has very often been studied independently from the mechanisms allowing coexistence. By considering the effects of dispersal and niche partitioning on diversity, the metacommunity perspective predicts a spatial scale-dependence of the shape of the relationship. Here, we present experimental evidence of such scale-dependent patterns. After approximately 500 generations of diversification in a spatially heterogeneous environment, we measured functional diversity (FD) and productivity at both local and regional scales in experimental source-sink metacommunities of the bacterium Pseudomonas fluorescens SBW25. At the regional scale, environmental heterogeneity yielded high levels of FD and we observed a positive correlation between diversity and productivity. At the local scale, intermediate dispersal increased local FD through a mass effect but there was no correlation between diversity and productivity. These experimental results underline the importance of considering the mechanisms maintaining biodiversity and the appropriate spatial scales in understanding its relationship with ecosystem functioning.

Protists have divergent effects on bacterial diversity along a productivity gradient

Productivity and predation are thought to be crucial drivers of bacterial diversity. We tested how the productivity-diversity of a natural bacterial community is modified by the presence of protist predators with different feeding preferences. In the absence of predators, there was a unimodal relationship between bacterial diversity and productivity. We found that three protist species (Bodo, Spumella and Cyclidium) had widely divergent effects on bacterial diversity across the productivity gradient. Bodo and Cyclidium had little effect on the shape of the productivity-diversity gradient, while Spumella flattened the relationship. We explain these results in terms of the feeding preferences of these predators.

Microbial cytotoxicity of carbon-based nanomaterials: implications for river water and wastewater effluent

This study evaluates the cytotoxicity of four carbon-based nanomaterials (CBNs)--single-walled carbon nanotubes (SWNTs), multiwalled carbon nanotubes (MWNTs), aqueous phase C60 nanoparticles (aq-nC60), and colloidal graphite--in gram negative and gram positive bacteria. The potential impacts of CBNs on microorganisms in natural and engineered aquatic systems are also evaluated. SWNTs inactivate the highest percentage of cells in monocultures of Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus epidermis, as well as in the diverse microbial communities of river water and wastewater effluent. Bacterial cytotoxicity displays time dependence, with longer exposure times accentuating toxicity in monocultures with initial tolerance for SWNTs. In Bacillus subtilis, an additional 3.5 h of incubation produced a five fold increase in toxicity. Elevated concentration of NOM reduces the attachment of bacteria on SWNT aggregates by 50%, but does not mitigate toxicity toward attached cells. CBN toxicity in bacterial monocultures was a poor predictor of microbial inactivation in chemically and biologically complex environmental samples.

Changes in microbial diversity in industrial wastewater evaporation ponds following artificial salination

The salinity of industrial wastewater evaporation ponds was artificially increased from 3-7% to 12-16% (w/v), in an attempt to reduce the activity of sulfate-reducing bacteria (SRB) and subsequent emission of H2S. To investigate the changes in bacterial diversity in general, and SRB in particular, following this salination, two sets of universal primers targeting the 16S rRNA gene and the functional apsA [adenosine-5'-phosphosulfate (APS) reductase alpha-subunit] gene of SRB were used. Phylogenetic analysis indicated that Proteobacteria was the most dominant phylum both before and after salination (with 52% and 68%, respectively), whereas Firmicutes was the second most dominant phylum before (39%) and after (19%) salination. Sequences belonging to Bacteroidetes, Spirochaetes and Actinobacteria were also found. Several groups of SRB from Proteobacteria and Firmicutes were also found to inhabit this saline environment. Comparison of bacterial diversity before and after salination of the ponds revealed both a shift in community composition and an increase in microbial diversity following salination. The share of SRB in the 16S rRNA gene was reduced following salination, consistent with the reduction of H2S emissions. However, the community composition, as shown by apsA gene analysis, was not markedly affected.

A latitudinal diversity gradient in planktonic marine bacteria

For two centuries, biologists have documented a gradient of animal and plant biodiversity from the tropics to the poles but have been unable to agree whether it is controlled primarily by productivity, temperature, or historical factors. Recent reports that find latitudinal diversity gradients to be reduced or absent in some unicellular organisms and attribute this to their high abundance and dispersal capabilities would suggest that bacteria, the smallest and most abundant organisms, should exhibit no latitudinal pattern of diversity. We used amplified ribosomal intergenic spacer analysis (ARISA) whole-assemblage genetic fingerprinting to quantify species richness in 103 near-surface samples of marine bacterial plankton, taken from tropical to polar in both hemispheres. We found a significant latitudinal gradient in richness. The data can help to evaluate hypotheses about the cause of the gradient. The correlations of richness with latitude and temperature were similarly strong, whereas correlations with parameters relating to productivity (chlorophyll, annual primary productivity, bacterial abundance) and other variables (salinity and distance to shore) were much weaker. Despite the high abundance and potentially high dispersal of bacteria, they exhibit geographic patterns of species diversity that are similar to those seen in other organisms. The latitudinal gradient in marine bacteria supports the hypothesis that the kinetics of metabolism, setting the pace for life, has strong influence on diversity.

Resource availability influences the diversity of a functional group of heterotrophic soil bacteria

Resource availability is a key factor regulating biodiversity and ecosystem functioning, but the relationship between resource availability and diversity has only been rarely investigated in microbial communities. The aim of this study was to determine how diversity and community structure of a functional group of soil bacteria are influenced by resource concentration. To achieve this, we used soil microcosms to investigate degradation of benzoate, which served as a model compound, by soil bacterial communities. Microcosms were supplied with (13)C-labelled benzoate at four concentrations and RNA-stable isotope probing followed by molecular fingerprinting analysis of 16S rRNA genes was employed to identify bacteria able to assimilate benzoate at different concentrations. The composition of the benzoate degrader community differed at different concentrations and there was a significant decrease in taxa evenness at the highest substrate concentration. Active organisms could be grouped into generalists, occurring at all substrate concentrations, specialists, active at one particular benzoate concentration only, and taxa that were active at either the two lowest or two highest concentrations. The study comprises the first explicit demonstration that resource availability has an effect on the diversity of a functional group of heterotrophic soil bacteria.