Halophilic microbial communities and their environments

Use of culture-independent studies have greatly increased our understanding of the microbiology of hypersaline lakes (the Dead Sea, Great Salt Lake) and saltern ponds in recent years. Exciting new information has become available on the microbial processes in Antarctic lakes and in deep-sea brines. These studies led to the recognition of many new lineages of microorganisms not yet available for study in culture, and their cultivation in the laboratory is now a major challenge. Studies of the metabolic potentials of different halophilic microorganisms, Archaea as well as Bacteria, shed light on the possibilities and the limitations of life at high salt concentrations, and also show their potential for applications in bioremediation.     

Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments

The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters treating lignocellulosic biomass such as straw. For that purpose, lignocellulose-degrading methanogenic communities were enriched on wheat straw from cow and goat rumen fluid as well as from a biogas reactor acclimated to lignocellulosic biomass (sorghum as mono-substrate). The bacterial communities of the enriched cultures and the different inocula were examined by 454 amplicon sequencing of 16S rRNA genes while the methanogenic archaeal communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the mcrA gene. Bacteroidetes was the most abundant phylum in all samples. Within the Bacteroidetes phylum, Bacteroidaceae was the most abundant family in the rumen-derived enrichment cultures, whereas Porphyromonadaceae was the predominant one in the reactor-derived culture. Additionally, the enrichment procedure increased the relative abundance of Ruminococcaceae (phylum: Firmicutes) in all cultures. T-RFLP profiles of the mcrA gene amplicons highlighted that the ruminal methanogenic communities were composed of hydrogenotrophic methanogens dominated by the order Methanobacteriales regardless of the host species. The methanogenic communities changed significantly during the enrichment procedure, but still the strict hydrogenotrophic Methanobacteriales and Methanomicrobiales were the predominant orders in the enrichment cultures. The bioaugmentation potential of the enriched methanogenic cultures will be evaluated in further studies.

     

Diversity and dynamics of microbial communities in soils from agro-ecosystems

Soil microbial communities are integrally involved in biogeochemical cycles and their activities are crucial to the productivity of terrestrial ecosystems. Despite the importance of soil microorganisms, little is known about the distribution of microorganisms in the soil or the manner in which microbial community structure responds to changes in land management. We investigated the structure of microbial communities in the soil over two years in a series of replicated plots, that included, cultivated fields, fields abandoned from cultivation and fields with no history of cultivation. Microbial community structure was examined by monitoring the relative abundance of ribosomal RNA (rRNA) from seven of the most common bacterial groups in soil (the Alpha and Beta Proteobacteria, Actinobacteria, Cytophagales, Planctomycetes, Verrucomicrobia and the Acidobacteria) and the Eukarya. These data reveal that soil microbial communities are dynamic, capable of significant change at temporal scales relative to seasonal events. However, despite temporal change in microbial community structure, the rRNA relative abundance of particular microbial groups is affected by the local environment such that recognizable patterns of community structure exist in relation to field management.     

Thermophilic microbial communities of deep-sea hydrothermal environments

The latest publications on the phylogenetic and functional diversity of thermophilic prokaryotes inhabiting thermal deep-sea environments are reviewed. Along with general physicochemical characterization of the biotope studied, certain adaptation mechanisms are discussed that are peculiar to the microorganisms inhabiting it. A separate chapter addresses phylogenetic analysis of deep-sea hydrothermal microbial communities and uncultivated microorganisms recently discovered therein using molecular biological techniques. Physiological groups of thermophilic microorganisms found in deep-sea hydrotherms are considered: methanogens, sulfate-, iron-, and sulfur-reducers, aerobic hydrogen-oxidizing prokaryotes, aerobic and anaerobic organotrophs. In most cases, the isolates represent novel taxa.     

Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef

The health and functioning of reef‐building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their diversity, ecological roles and responses to environmental stress, including ocean acidification (OA), are not well characterized. This study tests whether pH affects the diversity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp. using targeted amplicon (16S rRNA gene, UPA and tufA) sequencing. We found that the composition of endolithic communities in the massive coral Porites spp. inhabiting a naturally high pCO₂ reef (avg. pCO₂ 811 μatm) is not significantly different from corals inhabiting reference sites (avg. pCO₂ 357 μatm), suggesting that these microbiomes are less disturbed by OA than previously thought. Possible explanations may be that the endolithic microhabitat is highly homeostatic or that the endolithic micro‐organisms are well adapted to a wide pH range. Some of the microbial taxa identified include nitrogen‐fixing bacteria (Rhizobiales and cyanobacteria), algicidal bacteria in the phylum Bacteroidetes, symbiotic bacteria in the family Endozoicomoniaceae, and endolithic green algae, considered the major microbial agent of reef bioerosion. Additionally, we test whether host species has an effect on the endolithic community structure. We show that the endolithic community of massive Porites spp. is substantially different and more diverse than that found in skeletons of the branching species Seriatopora hystrix and Pocillopora damicornis. This study reveals highly diverse and structured microbial communities in Porites spp. skeletons that are possibly resilient to OA.     

Diversity, function and stability in parasitoid communities

The parasitoid assemblages associated with grass-feeding chalcid wasps in Great Britain were used to examine the relationships between diversity (species richness), community function (total parasitism rate) and stability (variability in parasitism rate over time). Species-rich communities did not generate higher parasitism rates than species-poor communities, nor was temporal variation of parasitism rates related to parasitoid community richness. The mechanisms underlying hypotheses linking species richness and community function and stability are discussed in the light of these results. Because all parasitoid species represent a single functional group, a lack of complementarity in the ways they use their resources may explain why diversity is not linked to function or community stability. A second likely reason is that these parasitoid communities are under bottom-up control, thus exerting little or no influence on total system function and variability. This is likely to be common in parasitoid communities.     

Functional stability of microbial communities in contaminated soils

Functional stability, measured in terms of resistance and resilience of respiration and growth rate of bacteria and fungi, was studied in soils that have been exposed to copper and low pH for more than twenty years. We used treatments, consisting of soil with no or high copper load (0 or 750 kg ha^?1) and low or neutral pH (4.0 or 6.1). Stability was examined by applying an additional stress in the form of lead or salt. After addition of lead, respiration (decomposition of freshly added lucerne meal) showed lower resistance at low than at neutral pH and at high copper than at low copper. The most acid and contaminated soil was the least resistant. Respiration showed no resilience after addition of lead. Bacterial growth rate (thymidine incorporation) also showed resistance at low pH but only in soils that were not contaminated with copper. After addition of salt, respiration showed no differences in resistance but the soils without copper contamination showed higher resilience. Bacterial growth rate showed lower resistance at low pH than at neutral pH, the latter in which the growth rate increased by on average 123%. This increase at high pH was faster in soil without copper than in soil with copper contamination in which the growth rate initially decreased and then increased. The effects of secondary stress depended on the nature of the stress (lead or salt) and on the parameter measured (respiration or bacterial growth rate). In general the highest resistance and/or resilience were found in the least contaminated soils with neutral pH and/or no copper contamination. Thus, the microbial communities in the cleaner soils showed the highest functional stability. The results seem to confirm the notion that environmental stress alters ecosystems such that supplementary stress will have stronger impacts than in an unstressed system. The results may also confirm the insurance‐hypothesis that reduced biodiversity due to the first stress negatively affected community stability. As an alternative, we discuss the observed effects in terms of altered energy budget.     

Genomic structure predicts metabolite dynamics in microbial communities

1. Download : Download high-res image (172KB)
2. Download : Download full-size image

     

Temporal dynamics of aquatic communities and implications for pond conservation

Conservation through the protection of particular habitats is predicated on the assumption that the conservation value of those habitats is stable. We test this assumption for ponds by investigating temporal variation in macroinvertebrate and macrophyte communities over a 10-year period in northwest England. We surveyed 51 ponds in northern England in 1995/6 and again in 2006, identifying all macrophytes (167 species) and all macroinvertebrates (221 species, excluding Diptera) to species. The alpha-diversity, beta-diversity and conservation value of these ponds were compared between surveys. We find that invertebrate species richness increased from an average of 29.5 species to 39.8 species between surveys. Invertebrate gamma-diversity also increased between the two surveys from 181 species to 201 species. However, this increase in diversity was accompanied by a decrease in beta-diversity. Plant alpha-, beta- and gamma-diversity remained approximately constant between the two periods. However, increased proportions of grass species and a complete loss of charophytes suggests that the communities are undergoing succession. Conservation value was not correlated between sampling periods in either plants or invertebrates. This was confirmed by comparing ponds that had been disturbed with those that had no history of disturbance to demonstrate that levels of correlation between surveys were approximately equal in each group of ponds. This study has three important conservation implications: (i) a pond with high diversity or high conservation value may not remain that way and so it is unwise to base pond conservation measures upon protecting currently-speciose habitats; (ii) maximising pond gamma-diversity requires a combination of late and early succession ponds, especially for invertebrates; and (iii) invertebrate and plant communities in ponds may require different management strategies if succession occurs at varying rates in the two groups.     

Diversity dynamics of echinoderms and evolution of marine communities

A compound analysis of two global paleontological databases (Sepkoski??s database (SDB) and The Paleobiology Database) allowed the recognition of a number of previously undescribed trends in the evolution of the phylum Echinodermata. Paleozoic echinoderms, dominated by sessile epibenthic filter feeders, played an important role in benthic communities, especially in the Ordovician and Carboniferous. Paleozoic echinoderms typically showed an increased rate of genus renewal, which significantly decreases in the Meso-Cenozoic. After the P-T crisis the echinoderms became dominated by motile taxa, while the role of infaunal forms increased. During the global turnover in the benthic communities at the K-T boundary, which was accompanied by a sharp increase in the mean alpha-diversity, many marine organisms became inhabitants of much richer (compared to the Mesozoic) communities. However, of all echinoderms, this trend is observed only in crinoids. In contrast to most large taxa, echinoderms do not show positive correlation between the duration of genera and alpha-diversity of communities, which included these genera. During the Phanerozoic the geographical distribution of echinoderms showed a sharp paleolatitudinal gradient, i.e., each period was characterized by one paleolatitudinal zone with the maximum diversity of echinoderms, and the diversity rapidly decreasing to the north and to the south of this zone. The zone of the maximum diversity of echinoderms, like of entire marine biota, during the Phanerozoic gradually moved from the tropics of the southern hemisphere to the middle latitudes of the northern hemisphere.     

Recurring seasonal dynamics of microbial communities in stream habitats

Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations associated with streambed sediments and rocks (epilithon) were identified using terminal restriction length polymorphism (tRFLP) and sequencing of 16S rRNA genes selectively amplified with primers for the bacterial domain. Analyses of the relative magnitudes of tRFLP peak areas by using nonmetric multidimensional scaling resolved clear seasonal trends in epilithic and sediment populations. Oscillations between two dominant groups of epilithic genotypes, explaining 86% of the seasonal variation in the data set, were correlated with temperature and dissolved organic carbon. Sequences affiliated with epilithic phototrophs (cyanobacteria and diatom chloroplasts), a Rhodoferax sp., and a Bacillus species clustered in the summer, whereas sequences most closely related to "Betaproteobacteria" (putative Burkholderia sp.), and a putative cyanobacterium clustered in the fall/spring. The sediment genotypes also clustered into two groups, and these explained 85% of seasonal variation but correlated only with temperature. A summer tRFLP pattern was characterized by prevalence of "Betaproteobacteria," "Gammaproteobacteria," and a Bacillus sp., whereas the winter/spring pattern was characterized by phylotypes most closely related to "Firmicutes," "Gammaproteobacteria," and "Nitrospirae." A close association between these headwater streams and their watersheds was suggested by the recovery of sequences related to microbial populations provisionally attributed to not only freshwaters but also terrestrial habitats.     

Drift dynamics in microbial communities and the effective community size

The structure and diversity of all open microbial communities are shaped by individual births, deaths, speciation and immigration events; the precise timings of these events are unknowable and unpredictable. This randomness is manifest as ecological drift in the population dynamics, the importance of which has been a source of debate for decades. There are theoretical reasons to suppose that drift would be imperceptible in large microbial communities, but this is at odds with circumstantial evidence that effects can be seen even in huge, complex communities. To resolve this dichotomy we need to observe dynamics in simple systems where key parameters, like migration, birth and death rates can be directly measured. We monitored the dynamics in the abundance of two genetically modified strains of Escherichia coli, with tuneable growth characteristics, that were mixed and continually fed into 10 identical chemostats. We demonstrated that the effects of demographic (non-environmental) stochasticity are very apparent in the dynamics. However, they do not conform to the most parsimonious and commonly applied mathematical models, where each stochastic event is independent. For these simple models to reproduce the observed dynamics we need to invoke an ‘effective community size’, which is smaller than the census community size.     

Thermodynamics of microbial growth and its implications for process design

Several different approaches have been used in an attempt to define and analyse the thermodynamics of microbial growth in bioreactor culture. While thermodynamic theory has been developed sufficiently to enable satisfactory prediction of biomass and catabolic-product yield, prediction of non-catabolicproduct yield and growth kinetics has proven less successful. Further research in this area is required to develop models that would be useful in process design and optimization.     

Diversity and similarity of microbial communities in petroleum crude oils produced in Asia

To understand microbial communities in petroleum crude oils, we precipitated DNA using high concentrations of 2,2,4-trimethylpentane (isooctane) and purified. Samples of DNA from five crude oils, (Middle East, 3; China, 1; and Japan, 1) were characterized based upon their 16S rRNA gene sequences after PCR amplification and the construction of clone libraries. We detected 48 eubacterial species, one cyanobacterium, and one archaeon in total. The microbial constituents were diverse in the DNA samples. Most of the bacteria affiliated with the sequences of the three oils from the Middle East comprised similar mesophilic species. Acinetobacter, Propionibacterium, Sphingobium and a Bacillales were common. In contrast, the bacterial communities in Japanese and Chinese samples were unique. Thermophilic Petrotoga-like bacteria (11%) and several anaerobic-thermophilic Clostridia- and Synergistetes-like bacteria (20%) were detected in the Chinese sample. Different thermophiles (12%) and Clostridia (2%) were detected in the Japanese sample.     

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.