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PubMed2002

Microbial diversity and function in soil: from genes to ecosystems.

Soils sustain an immense diversity of microbes, which, to a large extent, remains unexplored. A range of novel methods, most of which are based on rRNA and rDNA analyses, have uncovered part of the soil microbial diversity. The next step in the era of microbial ecology is to extract genomic, evolutionary and functional information from bacterial artificial chromosome libraries of the soil community genomes (the metagenome). Sophisticated analyses that apply molecular phylogenetics, DNA microarrays, functional genomics and in situ activity measurements will provide huge amounts of new data, potentially increasing our understanding of the structure and function of soil microbial ecosystems, and the interactions that occur within them. This review summarizes the recent progress in studies of soil microbial communities with focus on novel methods and approaches that provide new insight into the relationship between phylogenetic and functional diversity.

Bacteria↗

PubMed2004

Metamorphosis of a scleractinian coral in response to microbial biofilms.

Microorganisms have been reported to induce settlement and metamorphosis in a wide range of marine invertebrate species. However, the primary cue reported for metamorphosis of coral larvae is calcareous coralline algae (CCA). Herein we report the community structure of developing coral reef biofilms and the potential role they play in triggering the metamorphosis of a scleractinian coral. Two-week-old biofilms induced metamorphosis in less than 10% of larvae, whereas metamorphosis increased significantly on older biofilms, with a maximum of 41% occurring on 8-week-old microbial films. There was a significant influence of depth in 4- and 8-week biofilms, with greater levels of metamorphosis occurring in response to shallow-water communities. Importantly, larvae were found to settle and metamorphose in response to microbial biofilms lacking CCA from both shallow and deep treatments, indicating that microorganisms not associated with CCA may play a significant role in coral metamorphosis. A polyphasic approach consisting of scanning electron microscopy, fluorescence in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE) revealed that coral reef biofilms were comprised of complex bacterial and microalgal communities which were distinct at each depth and time. Principal-component analysis of FISH data showed that the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Cytophaga-Flavobacterium of Bacteroidetes had the largest influence on overall community composition. A low abundance of Archaea was detected in almost all biofilms, providing the first report of Archaea associated with coral reef biofilms. No differences in the relative densities of each subdivision of Proteobacteria were observed between slides that induced larval metamorphosis and those that did not. Comparative cluster analysis of bacterial DGGE patterns also revealed that there were clear age and depth distinctions in biofilm community structure; however, no difference was detected in banding profiles between biofilms which induced larval metamorphosis and those where no metamorphosis occurred. This investigation demonstrates that complex microbial communities can induce coral metamorphosis in the absence of CCA.

Animals↗

PubMed2005

Seasonal and management influences on bacterial community structure in an upland grassland soil.

Floristically diverse Nardo-Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement.

Bacteria↗

PubMed2004

Microbial diversity in inactive chimney structures from deep-sea hydrothermal systems.

Massive chimney structures, which are characteristic of many hydrothermally active zones, harbor diverse microbial communities containing both thermophilic and hyperthermophilic microbes. However, vent chimneys ultimately become hydrothermally inactive, and the changes that occur in the microbial communities upon becoming inactive have not been documented. We thus collected inactive chimneys from two geologically and geographically distinct hydrothermal fields, Iheya North in the western Pacific Ocean and the Kairei field in the Indian Ocean. The chimneys displayed easily distinguishable strata, which were analyzed with regard to both mineralogical and microbiological properties. X-ray diffraction pattern and energy-dispersive spectroscopic analyses revealed that the main mineral components of the chimney substructures from Iheya North and the Kairei field were barite (BaSO4) and chalcopyrite (CuFeS2), respectively. Microbial cell densities in the substructures determined by DAPI counting ranged from 1.7 x 10(7) cells g(-1) to 3.0 x 10(8) cells g(-1). The proportions of archaeal rDNA in the whole microbial rDNA assemblages in all substructures were, at most, a few percent as determined by quantitative fluorogenic PCR. The microbial rDNA clone analysis and whole-cell fluorescence in situ hybridization revealed a community that was decidedly different from any communities previously reported in active chimneys. Curiously, both samples revealed the abundant presence of a group of Bacteria related to a magnetosome-bearing bacterium, " Magnetobacterium bavaricum" of the Nitrospirae division. These results suggest that inactive chimneys provide a distinct microbial habitat.

Archaea↗

PubMed2006

The consequence of species loss on ecosystem nitrogen cycling depends on community compensation.

Repercussions of species loss on ecosystem processes depend on the effects of the lost species as well as the compensatory responses of the remaining species in the community. We experimentally removed two co-dominant plant species and added a 15N tracer in alpine tundra to compare how species' functional differences influence community structure and N cycling. For both of the species, production compensated for the biomass removed by the second year. However, the responses of the remaining species depended on which species was removed. These differences in compensation influenced how species loss impacted ecosystem processes. After the removal of one of the co-dominant species, Acomastylis rossii, there were few changes in the relative abundance of the remaining species, and differences in functioning could be predicted based on effects associated with the removed species. In contrast, the removal of the other co-dominant, Deschampsia caespitosa, was associated with subsequent changes in community structure (species relative abundances and diversity) and impacts on ecosystem properties (microbial biomass N, dissolved organic N, and N uptake of subordinate species). Variation in compensation may contribute to the resulting effects on ecosystem functioning, with the potential to buffer or accelerate the effects of species loss.

Analysis of Variance↗

PubMed2026

Postpartum compositional changes in bovine calf nasal and dam vaginal microbiota and concurrent immune responses following prepartum betadine lavages.

As interest in bovine reproductive tract microbial communities increases, there remains limited information on how the insult of parturition influences postpartum dam reproductive microbiota and early-life microbial development. The objective of this study was to characterize postpartum changes in dam vaginal microbiota and neonatal calf nasal microbiota following transient prepartum disruption of the dam vaginal microbiota using betadine lavages (BLGs), and to evaluate concurrent systemic immune responses in dams and calves. Multiparous beef cows (n = 12) were randomly assigned to either BLG (n = 7) or control (CON; n = 5) 3 wk prior to the expected calving date, and dam vaginal swabs, calf nasal swabs, and blood were collected at 0 (+1), 15 (±1), 30 (±1), and 60 (±1) d postpartum. Samples from Angus cow-calf pairs (n = 12) underwent 16S rRNA gene sequencing with standard contamination controls and QIIME2 processing. Blood samples were analyzed using the D2Dx immunity assay to evaluate systemic humoral immune responses. Microbial alpha diversity (ANOVA), Bray-Curtis beta diversity (PERMANOVA), taxonomic composition (LEfSe), and D2Dx immune responses (repeated-measures mixed model) were analyzed (P < 0.05). In calves, treatment influenced nasal alpha diversity at d 0 (P = 0.03), while nasal beta diversity tended to differ at d 0 (P = 0.08); however, treatment effects were not detected at d 15, 30, or 60 for alpha diversity (P ≥ 0.76) or beta diversity (P ≥ 0.14). Calf nasal communities shifted over time (P = 0.001), with d 0 differing from d 15, 30, and 60, and beta diversity differing over time (P = 0.006). In dams, BLG did not alter vaginal alpha diversity (P ≥ 0.42) or beta diversity (P ≥ 0.14) over time, and time did not affect vaginal alpha diversity (P = 0.60) while vaginal beta diversity tended to shift over time (P = 0.06). Postpartum dam vaginal and calf nasal communities differed compositionally regardless of time (P < 0.05). Systemic immune responses, measured via D2Dx scores, fluctuated postpartum in dams (day effect: P < 0.001) and calves (day effect: P < 0.001), with BLG calves tending toward decreased immune response compared with CON (P = 0.08). Prepartum BLG minimally influenced neonatal nasal microbial diversity at birth and did not alter postpartum dam vaginal community structure, while calf nasal microbiota and D2Dx immune responses changed markedly over the first 60 d of life.

Animals↗

PubMed2002

Cross-scale ecological dynamics and microbial size spectra in marine ecosystems.

Evaluating the component features of 'scaling' planktonic size spectra, commonly observed in marine ecosystems, is crucial for understanding the ecological and evolutionary processes from which they emerge. Here, we develop a theoretical framework that describes such spectra in terms of the size distributions of individual species, and test it against actual datasets of microbial size spectra from the Atlantic Ocean. We describe characteristics of size probability distributions of component species that are sufficient to support the observational evidence and infer that, when a power law describes the community size spectrum (thus suggesting critical self-organization of microbial ecosystem structure and function), a related power law links the total number of individuals of a given species to its mean size.

Animals↗

PubMed2006

[Biological fertility and its dynamics of degraded soil in Tibet Plateau].

In a three-year field trial, this paper studied the dynamics of biological fertility of degraded cultivated mountain shrubby steppe soil in the lower reaches of Lisa River as affected by fertilization. The results showed that under non-fertilized condition, the organic matter (OM) content in soil surface layer declined slightly, but after fertilization, the OM in this layer accumulated with a relatively high rate, humus structure improved obviously, soil bacteria had a significant multiplication, while soil microbial community was still in unharmonious state. With the increasing application rate of organic manure or chemical fertilizers, the OM content in 0 to approximately 30 cm and 30 to approximately 60 cm soil layers showed a significant increasing trend, with an annual increment being 1.35 and 0.67 g x kg(-1), respectively, and the ratio of humus carbon (C) to organic C and of humic acid C to humus C was also increased. Fertilization had a significant promotion effect on the multiplication and activity of soil bacteria. There was a significant positive correlation between the numbers of bacteria and OM content in 2 to approximately 30 cm (r = 0.7194 * *) and 30 to approximately 60 (r = 0.6042*) cm soil layers, while soil fungi and actinomycetes were not affected by fertilization. The numbers of azotobacter and cellulose-decomposing bacteria in different soil layers were lower in most fertilization treatments than in the control, and azotobacter in soil surface layer had a negative correlation with cellulose-decomposing bacteria (r = -0.4799).

Altitude↗

PubMed2002

Microbial communities and their interactions in soil and rhizosphere ecosystems.

Since the first estimate of prokaryotic abundance in soil was published, researchers have attempted to assess the abundance and distribution of species and relate this information on community structure to ecosystem function. Culture-based methods were found to be inadequate to the task, and as a consequence a number of culture-independent approaches have been applied to the study of microbial diversity in soil. Applications of various culture-independent methods to descriptions of soil and rhizosphere microbial communities are reviewed. Culture-independent analyses have been used to catalog the species present in various environmental samples and also to assess the impact of human activity and interactions with plants or other microbes on natural microbial communities. Recent work has investigated the linkage of specific organisms to ecosystem function. Prospects for increased understanding of the ecological significance of particular populations through the use of genomics and microarrays are discussed.

Archaea↗

PubMed2001

Dynamics of protozoan and metazoan communities in a full scale wastewater treatment plant by rotating biological contactors.

Performance of a full-scale wastewater treatment plant by rotating biological contactors (RBC) system was monitored during a year by physico-chemical and microbial characterisation. Six points along wastewater treatment were selected in the plant: three points along the water line (influent, sedimentation tank and effluent) and three points along RBC system (RBC1, RBC2 and RBC3). Although a large seasonal change in the values of physico-chemical parameters was observed, operation of the plant was optimal during all year (90% of removal in BOD5 and SS influent content). Microbial characterisation was approached by determining the structure and dynamics of protozoan and metazoan communities. Protozoa were the most abundant in all stages in the plant, heterotrophic flagellates being the most representative group in the water line and ciliates in the RBC system. The same seasonal preference was only observed for heterotrophic flagellates in the water line and green flagellates in the RBC system, both groups having highest abundances in summer and spring, respectively. Identification of ciliated protozoa populations rendered 58 species of ciliates in the plant. Most of these species are typical of aerobic wastewater treatment systems except three of them, which are cited for the first time in this type of ecosystems: Chaenea stricta, Holosticha mancoidea and Oxytricha lanceolata. Along the water line 34 species were identified, and half of them only appeared occasionally (once in all the study), while along the RBC system biofilms 55 species were observed, and the majority appeared permanently in this system. Our results indicate that the type of habitat, rather than the physico-chemical water parameters, was the primary factor in determining the different distribution of protozoan and metazoan communities in the plant. In RBC biofilms, the structure of ciliate protozoa community was found to be quite sensitive to changes in physico-chemical parameters, mainly to organic loading (BOD5) variations.

Amoeba↗

PubMed2005

Community structure and diversity of biofilms from a beer bottling plant as revealed using 16S rRNA gene clone libraries.

The microbial composition of biofilms from a beer bottling plant was analyzed by a cultivation independent analysis of the 16S rRNA genes. Clone libraries were differentiated by amplified 16S rRNA gene restriction analysis and representative clones from each group were sequenced. The diversity of the clone libraries was comparable with the diversity found for environmental samples. No evidences for the presence of strictly anaerobic taxa or important beer spoilers were found, indicating that biofilms developed for more than 6 months at the plant formed no appropriate habitat for those microorganisms. The genus Methylobacterium was one of the dominating groups of the clone libraries. The size of this population was assessed by fluorescence in situ hybridization and fatty acid analysis. In addition, considerable numbers of clones were assigned to uncultivated organisms.

Bacteria↗

PubMed2001

16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots.

Molecular techniques employing 16S rDNA profiles generated by PCR-DGGE were used to detect changes in bacterial community structures of the rhizosphere of avocado trees during infection by Phytophthora cinnamomi and during repeated bioaugmentation with a disease suppressive fluorescent pseudomonad. When the 16S rDNA profiles were analyzed by multivariate analysis procedures, distinct microbial communities were shown to occur on healthy and infected roots. Bacterial communities from healthy roots were represented by simple DNA banding profiles, suggestive of colonization by a few predominant species, and were approximately 80% similar in structure. In contrast, roots that were infected with Phytophthora, but which did not yet show visible symptoms of disease, were colonized by much more variable bacterial communities that had significantly different community structures from those of healthy roots. Root samples from trees receiving repeated applications of the disease suppressive bacterium Pseudomonas fluorescens st. 513 were free of Phytophthora infection, and had bacterial community structures that were similar to those of nontreated healthy roots. Sequence analysis of clones generated from four predominant bands cut from the DGGE gels revealed the presence of pseudomonads, as well as several previously unidentified bacteria. Differentiation of 16S rDNA profiles for healthy and infected roots suggests that rhizosphere bacterial community structure may serve as an integrative indicator of changes in chemical and biological conditions in the plant rhizosphere during the infection process.

Journal Article↗

PubMed1998

rRNA-targeted fluorescent in situ hybridization analysis of bacterial community structure in river water.

An improved in situ hybridization technique, HNPP-FISH, using 2-hydroxy-3-naphthoic acid 2'-phenylanilide phosphate (HNPP) and Fast Red TR was applied to analyse the community structure of planktonic bacteria in river water. Oligonucleotide probes specific for the domain Bacteria (EUB338) and five bacterial groups [Flavobacterium-Cytophaga; Burkholderia-Pseudomonas (rRNA III)-authentic Alcaligenes; Vibrio-Aeromonas; Pseudomonas (rRNA I): the genus Acinetobacter] were used to investigate the bacterial community structure at two sites differing in organic carbon pollution level. At the eutrophic site, 54-68% of all cells visualized by staining with DAPI (4',6-diamidino-2-phenylindole) could be detected with probe EUB338. In samples from the oligotrophic site, 39-45% of the total cells hybridized with EUB338. At the eutrophic site, approximately 50% of the total cells were identified with the five group-specific probes; the bacterial community structure was dominated by the Flavobacterium-Cytophaga group and Burkholderia-Pseudomonas (rRNA III)-authentic Alcaligenes group. At the oligotrophic site, only 26-38% of the total cells were identified with the five group-specific probes. The community structure at the oligotrophic site was similar to that at the eutrophic site, although the percentage of EUB338-detectable cells differed. No appreciable change was found in the community structure during the sampling period at either site. The improved HNPP-FISH technique should be a useful tool for the analysis of microbial community composition.

Bacteria↗

PubMed1998

Novel techniques for analysing microbial diversity in natural and perturbed environments.

Molecular techniques were applied for analysing the entire bacterial community, including both the cultivated and non-cultivated part of the community. DNA was extracted from samples of soils and sediments, and a combination of different molecular methods were used to investigate community structure and diversity in these environments. Reassociation of sheared and thermally denatured DNA in solution was used to measure the total genetical diversity. PCR-denaturing gradient gel electrophoresis (DGGE) analysis of rRNA genes gave information about changes in the numerically dominating bacterial populations. Hybridisation with phylogenetic group specific probes, and sequencing provided information about the affiliation of the bacterial populations. Using DNA reassociation analysis we demonstrated that bacterial communities in pristine soil and sediments may contain more than 10,000 different bacterial types. The diversity of the total soil community was at least 200 times higher than the diversity of bacterial isolates from the same soil. This indicates that the culturing conditions select for a distinct subpopulation of the bacteria present in the environment. Molecular methods were applied to monitor the effects of perturbations due to antropogenic activities and pollution on microbial communities. Our investigations show that agricultural management, fish farming and pollution may lead to profound changes in the community structure and a reduction in the bacterial diversity.

Bacteria↗

PubMed2006

Genomics for environmental microbiology.

The utilization of natural microbial diversity in biotechnology is hindered by our inability to culture the vast majority of microorganisms and the observation that laboratory engineered bacteria rarely function in the wild. It is now clear that an understanding of the community structure, function and evolution of bacteria in their natural environments is required to meet the promise of microbial biotechnology. To meet these new challenges, microbiologists are applying the tools of genomics and related high-throughput technologies to both cultured microbes and environmental samples. This work will lead to new views on ecosystems and biological function together with the biotechnology enabled by this science.

Environmental Microbiology↗

PubMed2004

Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate.

Previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. Microbial communities were stimulated in the acidic subsurface by pH neutralization and addition of an electron donor to wells. In single-well push-pull tests at a number of treated sites, nitrate, Fe(III), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. Examination of sediment chemistry in cores sampled immediately adjacent to treated wells 3.5 months after treatment revealed that sediment pH increased substantially (by 1 to 2 pH units) while nitrate was largely depleted. A large diversity of 16S rRNA gene sequences were retrieved from subsurface sediments, including species from the alpha, beta, delta, and gamma subdivisions of the class Proteobacteria, as well as low- and high-G+C gram-positive species. Following in situ biostimulation of microbial communities within contaminated sediments, sequences related to previously cultured metal-reducing delta-Proteobacteria increased from 5% to nearly 40% of the clone libraries. Quantitative PCR revealed that Geobacter-type 16S rRNA gene sequences increased in biostimulated sediments by 1 to 2 orders of magnitude at two of the four sites tested. Evidence from the quantitative PCR analysis corroborated information obtained from 16S rRNA gene clone libraries, indicating that members of the delta-Proteobacteria subdivision, including Anaeromyxobacter dehalogenans-related and Geobacter-related sequences, are important metal-reducing organisms in acidic subsurface sediments. This study provides the first cultivation-independent analysis of the change in metal-reducing microbial communities in subsurface sediments during an in situ bioremediation experiment.

Bacteria↗

PubMed2006

Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach.

Escherichia coli is a model laboratory bacterium, a species that is widely distributed in the environment, as well as a mutualist and pathogen in its human hosts. As such, E. coli represents an attractive organism to study how environment impacts microbial genome structure and function. Uropathogenic E. coli (UPEC) must adapt to life in several microbial communities in the human body, and has a complex life cycle in the bladder when it causes acute or recurrent urinary tract infection (UTI). Several studies designed to identify virulence factors have focused on genes that are uniquely represented in UPEC strains, whereas the role of genes that are common to all E. coli has received much less attention. Here we describe the complete 5,065,741-bp genome sequence of a UPEC strain recovered from a patient with an acute bladder infection and compare it with six other finished E. coli genome sequences. We searched 3,470 ortholog sets for genes that are under positive selection only in UPEC strains. Our maximum likelihood-based analysis yielded 29 genes involved in various aspects of cell surface structure, DNA metabolism, nutrient acquisition, and UTI. These results were validated by resequencing a subset of the 29 genes in a panel of 50 urinary, periurethral, and rectal E. coli isolates from patients with UTI. These studies outline a computational approach that may be broadly applicable for studying strain-specific adaptation and pathogenesis in other bacteria.

Chromosomes, Bacterial↗

PubMed2000

Spatial Organization of Microbial Biofilm Communities.

The application of advanced microscopy and molecular and electrochemical high-resolution methods has provided insights into the structural organization and function of biofilm communities. It appears that cellular properties such as growth differentiation, chemotaxis, and cell-to-cell signaling enable biofilm communities to organize structurally in response to the external conditions and the activities of the different biofilm members. Thereby resource utilization becomes optimized, and processes which require syntrophic relationships or special micro-environments become facilitated.

Journal Article↗