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PubMedDate not supplied

[Influence of different ecological groups of earthworms on the intensity of nitrogen fixation].

The results of studying nitrogen fixation in organic substrates processed by different ecological groups of earthworms suggest that the earthworms Aporrectoidea caliginosa actively stimulate nonsymbiotic nitrogen fixation. In this respect, they exceed the manure worms Eizenia foetida tens of times due to the formation in the organic substrate of conditions favorable for the nitrogen fixing bacteria, and namely: low content of nitrogen easily accessible for microorganisms, changes in the structure of the microbial community of the substrate in favor of non-spore forms of bacteria, and suppression of the growth of saprophyte bacilli, the main competitors of nitrogen fixing bacteria for carbon nourishment sources.

Animals↗

PubMed2006

Site-specific variation in Antarctic marine biofilms established on artificial surfaces.

The community structure and composition of marine microbial biofilms established on glass surfaces was investigated across three differentially contaminated Antarctic sites within McMurdo Sound. Diverse microbial communities were revealed at all sites using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) techniques. Sequencing of excised DGGE bands demonstrated close affiliation with known psychrophiles or undescribed bacteria also recovered from the Antarctic environment. The majority of bacterial sequences were affiliated to the Gammaproteobacteria, Cytophaga/Flavobacteria of Bacteroidetes (CFB), Verrucomicrobia and Planctomycetales. Principal components analysis of quantitative FISH data revealed distinct differences in community composition between sites. Each of the sites were dominated by different bacterial groups: Alphaproteobacteria, Gammaproteobacteria and CFB at the least impacted site, Cape Armitage; green sulfur and sulfate reducing bacteria near the semi-impacted Scott Base and Planctomycetales and sulfate reducing bacteria near the highly impacted McMurdo Station. The highest abundance of archaea was detected near Scott Base (2.5% of total bacteria). Multivariate analyses (non-metric multidimensional scaling and analysis of similarities) of DGGE patterns revealed greater variability in community composition between sites than within sites. This is the first investigation of Antarctic biofilm structure and FISH results suggest that anthropogenic impacts may influence the complex composition of microbial communities.

Actinobacteria↗

PubMed2003

Microbial spheres: a novel cyanobacterial-diatom symbiosis.

Cyanobacteria, algae and bacteria are widespread inhabitants of North Sea microbial mats. Our studies of these populations showed uncommon modes of living and extraordinary structures, which have not been described before. The structures are spherical objects covering a community of cyanobacteria, diatoms and bacteria. The cultivation of these communities in the laboratory and intensive observations of their exceptional movement has led to some spectacular findings. The sphere formations go through different phases with variation in the dominance of different microorganisms. The role of the bacteria is the most important in the first phase, and can be increased by the addition of signal substances. Spheres surrounded by envelopes of unknown composition and permeability appear, with numerous bacteria and sporadic diatoms inside. Then the cyanobacteria penetrate the spheres and arrange themselves at the surface. The communities proliferate over some weeks and are finally released. Laboratory expositions of the microbial communities to different parameters pinpoint the limits of sphere formation. The metabolic products of the sphere communities are concentrated in the spheres and lead to a different kind of compound compared with the surrounding environment. In this way, the microbial communities strongly influence the structure of the sediments. Uncommon circular structures, which develop into spheres between 0.08 and 3 mm in size were found in subcultures of non-axenic filamentous cyanobacteria enrichments from North Sea microbial mats. These filamentous cyanobacteria ( Phormidium sp.) together with associated benthic diatoms of the genus Navicula and associated heterotrophic bacteria were held as reproducible synergistic cultures. Phormidium sp. filaments tightly intertwined with each other, formed the surface of the spheres, trapping diatoms inside. The formation of "spheres" was the result of radial and synchronous movements of the cyanobacteria. In old cultures, the direction of the cyanobacterial movement has turned in the opposite direction, away from the sphere. The integrity of large "spheres" was influenced by chemotactic phenomena and maintained by some type of trichome-trichome interaction. This suggests the presence of metabolic secondary products, which attract cyanobacteria and influence their movement in a form of chemotactic response.

Cyanobacteria↗

PubMed2026

Unveiling microbial communities and biogeochemical cycles in Antarctic colored snow.

Snow cover, the extensive terrestrial habitat in Antarctica, sometimes exhibits vivid coloration, yet the structure and function of its microbial communities remain poorly characterized. Using metagenomic sequencing of red snow (RS) and green snow (GS) from the Fildes Peninsula, we found that bacterial, eukaryotic, and archaeal relative abundances were 85.82%, 13.52% and 0.16%, respectively. β-Diversity differed significantly between RS and GS across these three domains (P < 0.05). Dominant bacterial phyla included Bacteroidota (RS: 62.61%; GS: 38.72%) and Pseudomonadota (RS: 32.80%; GS: 54.10%). Among eukaryotes, Chlorophyta (RS: 58.10%; GS: 52.98%) and Basidiomycota (RS: 14.80%; GS: 8.08%) were prevalent. Nanobdellota dominated archaea, with lower abundance in RS than GS. In the algal community, Sanguina, Gonium and Chloromonas were significantly enriched in red snow, while Chlorella and Micractinium were enriched in green snow (P < 0.05). Marker genes associated with carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles were identified in green and red snow. Aerobic respiration and phosphate regulation were significantly enriched in red snow, while CO oxidation, fermentation, and denitrification were significantly enriched in green snow. Key microbial genera associated with these functional pathways also varied. In the denitrification of red snow, Stutzerimonas was the most abundant genus, while Janthinobacterium was abundant in green snow. Nitrification-related genes were detected only in red snow based on the present metagenomic data. The network of the red snow microbial community was potentially more complex and resistant based on topology, which not only benefited its own long-term survival but might also have potentially influenced the positive feedback effect of snowmelt by maintaining a low-albedo snow surface. This provided an ecological implication under climate warming: the expansion of red snow patches showed the potential to the increase nitrate runoff export, which would affect nitrogen nutrient levels in coastal Antarctic waters. Overall, this study used metagenomics to compare the multidomain (bacteria, archaea and eukaryotes) composition and diversity between red snow and green snow, and directly linked key microbial taxa with functional genes of biogeochemical cycles. This study provided new insights into the biological characteristics and functional potential of Antarctic colored snow.

Snow↗

PubMed2005

Variability in microbial community and venting chemistry in a sediment-hosted backarc hydrothermal system: Impacts of subseafloor phase-separation.

Phase-separation and -segregation (boiling/distillation of subseafloor hydrothermal fluids) represent the primary mechanisms causing intra-field variations in vent fluid compositions. To determine whether this geochemical process affects the formation of microbial communities, we examined the microbial communities at three different vent sites located within a few tens meters of one another. In addition to chimney structures, colonization devices capturing subseafloor communities entrained by the vent fluids were studied, using culture-dependent and -independent methods. Microbiological analyses demonstrated the occurrence of distinctive microbial communities in each of the hydrothermal niches. Within a chimney structure, there was a transition from a mixed community of mesophiles and thermophiles in the exterior parts to thermophiles in the interior. Beside the transition within a chimney structure, intra-field variations in microbial communities in vent fluids were apparent. Geochemical analysis demonstrated that different vent fluids have distinctive end-member compositions as a consequence of subseafloor phase-separation and -segregation, which were designated gas-depleted, normal and gas-enriched fluids. In comparison to gas-depleted and normal fluids, gas-enriched fluids harbored more abundant chemolithoautotrophs with gaseous component-dependent energy metabolism, such as hydrogenotrophic methanogenesis. Subseafloor phase-separation and -segregation may play a key role in supplying energy and carbon sources to vent-associated chemolithoautotrophs and subvent microbial communities.

Archaea↗

PubMed2006

Alteration and resilience of the soil microbial community following compost amendment: effects of compost level and compost-borne microbial community.

Compost amendment has been reported to impact soil microbial activities or community composition. However, little information is available on (i) to what extent compost amendment concurrently affects the activity, size and composition of soil microbial community, (ii) the relative effect of the addition of a material rich in organic matter versus addition of compost-borne microorganisms in explaining the effects of amendment and (iii) the resilience of community characteristics. We compared five treatments in microcosms: (i) control soil (S), (ii) soil + low level of compost (Sc), (iii) soil + high level of compost (SC), (iv) sterilized soil + high level of compost [(S)C] and (v) soil + high level of sterilized compost [S(C)]. The actual C mineralization rate, substrate-induced respiration, size of microbial community (biomass and heterotrophic cells number), and structure of total microbial (phospholipid fatty acids) and bacterial (automated ribosomal intergenic spacer analysis, A-RISA) communities were surveyed during 6 months after amendment. Our results show that (i) compost amendment affected the activity, size and composition of the soil microbial community, (ii) the effect of compost amendment was mainly due to the physicochemical characteristics of compost matrix rather than to compost-borne microorganisms and (iii) no resilience of microbial characteristics was observed 6-12 months after amendment with a high amount of compost.

Bacteria↗

PubMed2007

Effect of dilution rate on the microbial structure of a mesophilic butyrate-degrading methanogenic community during continuous cultivation.

We constructed two mesophilic anaerobic chemostats that were continuously fed with synthetic wastewater containing butyrate as the sole source of carbon and energy. Steady-state conditions were achieved at dilution rates between 0.025 and 0.7 day(-1). Butyrate, fed into the chemostat, was almost completely mineralized to CH(4) and CO(2) at dilution rates below 0.5 day(-1). The butyrate-degrading methanogenic communities in the chemostats at dilution rates between 0.025 and 0.7 day(-1) were monitored based on the 16S rRNA gene, using molecular biological techniques including clone library analysis, denaturing gradient gel electrophoresis, and quantitative real-time polymerase chain reaction. The aceticlastic methanogen Methanosaeta and the hydrogenotrophic methanogen Methanoculleus dominated in methanogens at low dilution rates, whereas the aceticlastic methanogen Methanosaeta, Methanosarcina, the hydrogenotrophic methanogen Methanoculleus, and Methanospirillum dominated at high dilution rates. Bacteria affiliated with the family Syntrophaceae in the phylum Proteobacteria predominated at the low dilution rate of 0.025 day(-1), whereas bacteria affiliated with the phylum Firmicutes and Candidate division OP3 predominated at high dilution rates. A significant quantity of bacteria closely related to the genus Syntrophomonas was detected at high dilution rates. Dilution rate showed an apparent effect on archaeal and bacterial communities in the butyrate-fed chemostats.

Bacteria↗

PubMed2000

An in situ respirometric technique to measure pollution-induced microbial community tolerance in soils contaminated with 2,4, 6-trinitrotoluene.

Long-term exposure to 2,4,6-trinitrotoluene (TNT) can induce changes in the structure and activities of soil microbial communities. Such changes may be associated with an elevated microbial tolerance. An in situ respirometry technique based on the analysis of the substrate-induced respiration response to freshly added TNT was used to examine soil microbial tolerance to TNT at the community level. The specific growth rate derived by fitting an exponential equation to respiration data was taken as the measurement endpoint. Microbial tolerance was evaluated using a tolerance index defined as the ratio of the specific growth rate at a spiking dose of 2000 microg TNT/g soil to that of the control with no spiked TNT. Three soils with long-term exposure histories (TNT level in soil: 1.5, 32, and 620 microg TNT/g, respectively) exhibited significantly higher microbial community tolerance to TNT than two uncontaminated control soils. A soil containing 29,000 microg TNT/g exhibited the highest tolerance. Findings from this study support the hypothesis that pollution-induced community tolerance can be used as a means of identifying those compounds that have exerted selective pressure on the community.

Dose-Response Relationship, Drug↗

PubMed2005

Niche heterogeneity determines bacterial community structure in the termite gut (Reticulitermes santonensis).

Differences in microenvironment and interactions of microorganisms within and across habitat boundaries should influence structure and diversity of the microbial communities within an ecosystem. We tested this hypothesis using the well characterized gut tract of the European subterranean termite Reticulitermes santonensis as a model. By cloning and sequencing analysis and molecular fingerprinting (terminal restriction fragment length polymorphism), we characterized the bacterial microbiota in the major intestinal habitats - the midgut, the wall of the hindgut paunch, the hindgut fluid and the intestinal protozoa. The bacterial community was very diverse (> 200 ribotypes) and comprised representatives of several phyla, including Firmicutes (mainly clostridia, streptococci and Mycoplasmatales-related clones), Bacteroidetes, Spirochaetes and a number of Proteobacteria, all of which were unevenly distributed among the four habitats. The largest group of clones fell into the so-called Termite group 1 (TG-1) phylum, which has no cultivated representatives. The majority of the TG-1 clones were associated with the protozoa and formed two phylogenetically distinct clusters, which consisted exclusively of clones previously retrieved from the gut of this and other Reticulitermes species. Also the other clones represented lineages of microorganisms that were exclusively recovered from the intestinal tract of termites. The termite specificity of these lineages was underscored by the finding that the closest relatives of the bacterial clones obtained from R. santonensis were usually derived also from the most closely related termites. Overall, differences in diversity between the different gut habitats and the uneven distribution of individual phylotypes support conclusively that niche heterogeneity is a strong determinant of the structure and spatial organization of the microbial community in the termite gut.

Animals↗

PubMed1981

Simulation of the rat intestinal ecosystem using a two-stage continuous culture system.

To investigate the ecological mechanisms governing the community structure of the gut microbial ecosystem, we have attempted to simulate the rat gut ecosystem in vitro using a two-stage continuous culture. Extensive sampling of the rat hindgut has established a set of criteria with which the in vitro system may be compared. This paper discusses one of the criteria, the community composition and structure in vivo and in vitro. The experiments indicated that a gut microbial ecosystem could be satisfactorily mimicked in vitro. This was achieved using a two-stage continuous culture employing differential selection of species between the two stages on the basis of pH differences combined with cell recycling between stages.

Animals↗

PubMed1996

S Cycling: Characterization of Natural Communities of Sulfate-Reducing Bacteria by 16S rRNA Sequence Comparisons

Past studies of microbial communities responsible for geochemical transformations have been limited by an inability to representatively cultivate, and then identify, the constituent members. Ribosomal RNA sequences, particularly 16S-like rRNAs, provide a measure of phylogenetic relationship that can now be used to examine the structure and diversity of microbial communities. Sulfate-reducing bacteria (SRB) play an important role in the sulfur cycle and the terminal mineralization of organic matter in estuarine and marine environments. Because the Gram-negative mesophilic SRB comprise a phylogenetically coherent assemblage, their communities are well suited to explorations through rRNA sequence-based methodologies. In this study we related molecular biological methods using rRNA probes to geochemical measurements at two different sites. At an unvegetated site in northwest Florida, rates of sulfate reduction were low and SRB rRNA comprised about 5% of the total rRNA extracted from the sediment. The other site, a salt marsh in New Hampshire, had higher rates of sulfate-reduction with SRB rRNA accounting for up to 30% of the total rRNA extracted from the sediment. SRB community structure differed dramatically between the two sites with Desulfobulbus rRNA much less abundant in the unvegetated site than in the salt marsh. The differences in these SRB communities reflect differences in the ecology of their habitats.

Journal Article↗

PubMed2005

New approaches for the characterization of prosthetic joint biofilms.

Indwelling prosthetic joints may become colonized by microbial biofilms, although the biofilm structure, composition of the microbial community, and physiologic activity of the organisms in these devices are not well understood. New approaches that rely on the use of fluorescent stain technology can be used to characterize the structure and community composition in a way that earlier methods, which relied on culturing or scanning electron microscopy, could not. Model systems incorporating parameters relevant for indwelling prosthetic joints also can be designed to evaluate the efficacy of treatments for preventing or eradicating biofilms from these devices. Effectively treating microbial biofilms on indwelling medical devices such as prosthetic joints is a challenging proposition. A clearer understanding of the process in vivo and a defined approach for evaluating treatment strategies provide the best hope for success.

Biofilms↗

PubMed2005

Impacts of methamidophos, copper, and their combinations on bacterial community structure and function in black soil.

The potential ecotoxicologial risks of methamidophos, copper, and their combinations on microbial community of black soil ecosystem in the Northeast China were assessed in species richness and structures by using 16S rDNA-PCR-DGGE analysis approach, and functional characteristics at community levels by using BIOLOG(GN) system analysis method as well as two conventional methods (DHA and SIR). All results of DGGE banding fingerprint patterns (amplified by bacterial specific 16S rDNA V3 high variable region universal primer) indicated that the species richness of bacterial community in tested soil was significantly decreased to different extents by using different concentrations of single methamidophos, copper, especially some of their combinations had worse effects than their corresponding single factors. In addition, the structures of soil bacterial community had been disturbed under all stresses applied in this study because of the enrichment of some species and the disappearance of other species from the bacterial community. The effects of the single factors with lower concentrations on the community structure were weaker than those with higher concentrations. Moreover, the bacterial community structures under the combined stresses of methamidophos and copper were significantly different from those of control and their corresponding single factors. The change of DHA and carbon source substrate utilizing fingerprint patterns based on BIOLOG(GN) system were two relatively sensitive directors corresponding to the stress presented in this study. Between methamodophos and copper, there happened the significant joint-toxic actions when they were used in combination on DHA and carbon source substrate utilizing fingerprint patterns of soil bacterial communities. The DHA of soil under the combined stresses was lower than that of the control and that under the single factors, and the BIOLOG(GN) substrate utilizing patterns of soil treated by combinations were distinctively differentiated from the control and their corresponding single factors. From all of above, the methamidophos, copper, especially their combinations had the clearly potential ecotoxicological risks to influence the natural soil microbial ecological system by changing the structure, richness, and the functional characteristics of microbial community.

Bacteria↗

PubMed1995

Molecular genetic analysis of the response of three soil microbial communities to the application of 2,4-D.

The responses of three different soil microbial communities to the experimental application of 2,4-dichlorophenoxyacetic acid (2,4-D) were evaluated with a variety of molecular genetic techniques. Two of the three soil communities had histories of prior direct exposure to 2,4-D, and one had no prior direct application of any herbicide. Dominant 2,4-D degrading strains isolated from these soils the previous year were screened for hybridization with three catabolic genes (tfdA, tfdAII, and tfdB) cloned from the well-studied 2,4-D degradative plasmid, pJP4, revealing varying degrees of similarity with the three genes. Hybridization of total community DNA from the three soils with the tfd gene probes also indicated that pJP4-like tfd genes were not harboured by a significant percentage of the community. Community level response was evaluated by the comparison of different treatments by Random Amplified Polymorphic DNA (RAPD) fingerprints and by community DNA cross-hybridization. No differences between treatments within the same soil were detected in any of the RAPD fingerprints generated with 17 primers. Community DNA cross-hybridization also indicated that the application of 2,4-D at the applied rates did not quantitatively affect the structure of the soil microbial communities present in the three soils during the time-frame studied.

2,4-Dichlorophenoxyacetic Acid↗

PubMed2002

Maintenance and impacts of an inoculated mer/luc-tagged Pseudomonas fluorescens on microbial communities in birch rhizospheres developed on humus and peat.

Antagonistic bacteria represent promising biocontrol agents for improving forest production in seedling nurseries or forest soils. The fate of an introduced mer/luc-tagged antagonistic Pseudomonas fluorescens 31K3 was monitored in the rhizosphere of silver birch (Betula pendula) seedlings grown in microcosms containing forest humus or nursery peat. The inoculated strain (10(8) cfu g(-1) soil) was unable to establish in significant numbers in either soil type and turned nonculturable in humus. Detection in both soils was possible only via luminescence of enrichment cultures 80 days post-inoculation. Despite low P. fluorescens survival, inoculation had a positive effect on seedling growth. Limited impact of inoculation on the indigenous microbial communities was identified following analyses of respiration and denitrification potential, community-level physiological profiles and molecular fingerprinting of fungi and eubacteria, and Pseudomonas community structures. The minor changes observed in the indigenous microbial communities, including mycorrhiza development, were not consistent between humus and peat growth substrates. It was concluded that the rhizosphere-related microbial communities developed in both of these highly organic soil systems are highly buffered against introduction of foreign bacteria.

Betula↗

PubMed1997

Effects of Recreational Impacts on Soil Microbial Communities

/ The functional diversity of soil microbial communities in heavilyimpacted subalpine campsites and adjacent undisturbed areas was comparedusing the Biolog method of carbon utilization profiles. Principal componentsanalysis of patterns and level of microbial activity indicate that microbialcommunities differentiate in response to disturbance in the top 6 cm of soil,while below 6 cm there were no recognizable differences between disturbed andundisturbed soil communities. Analysis of the factors that differentiate theupper microbial communities between disturbed and undisturbed sites revealedthat the percent of total carbon sources utilized was significantly less inthe disturbed (54%) than in undisturbed areas (95%). Carbonsubstrates important in the discrimination between soil communities includeplant, invertebrate, and microbial derivatives that could not be metabolizedby microbial communities from disturbed sites. Comparisons of totalculturable actinomycetes, bacteria, and fungi reveal no difference in overallnumber of colony forming units (CFU) on disturbed and undisturbed sites, buta marked decrease in actinomycetes on disturbed sites. Biolog andspread-plate data combined indicate a shift in the structure and function ofthe microbial community in campsite soils, which may be a useful indicator ofsoil community disturbance.KEY WORDS: Microbial functional diversity; Anthropogenic disturbance;Recreational impacts; Carbon source profile; Subalpine

Journal Article↗

PubMedDate not supplied

[The classification and the monitoring of the state of mouth riverine and lacustrine ecosystems in lake Baikal based on the composition of local microbiocenoses and their activity].

The paper presents the results of the long-term investigation of microbial communities in the technogenically vulnerable mouth riverine and lacustrine ecosystems of Lake Baikal. The structural and functional parameters of the microbial communities were analyzed from the standpoint of developing destructive processes. The analysis showed that the total number of microorganisms (TNM), the number of saprophytic bacteria (NSB), and bacterial production (BP) were greater in the river-mouth water than in the near-mouth lake water. In the offshore direction, TNM and NSB decreased by a factor of 1.5 to 2, and BP decreased by a factor of 4 to 7. Based on TNM, NSB, and BP data, we classified the Lake Baikal rivers with respect to the degree of the impact of human activities on them. The degrading capability of the riverine microbial communities was found to be such that they degrade daily from tenths of a percent to 3.5% of the total amount of organic compounds polluted the river waters.

Bacteria↗

PubMed2004

Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge.

The recently discovered Lost City Hydrothermal Field (LCHF) represents a new type of submarine hydrothermal system driven primarily by exothermic serpentinization reactions in ultramafic oceanic crust. Highly reducing, alkaline hydrothermal environments at the LCHF produce considerable quantities of hydrogen, methane and organic molecules through chemo- and biosynthetic reactions. Here, we report the first analyses of microbial communities inhabiting carbonate chimneys awash in warm, high pH fluids at the LCHF and the predominance of a single group of methane-metabolizing Archaea. The predominant phylotype, related to the Methanosarcinales, formed tens of micrometre-thick biofilms in regions adjacent to hydrothermal flow. Exterior portions of active structures harboured a diverse microbial community composed primarily of filamentous Eubacteria that resembled sulphide-oxidizing species. Inactive samples, away from regions of hydrothermal flow, contained phylotypes related to pelagic microorganisms. The abundance of organisms linked to the volatile chemistry at the LCHF hints that similar metabolic processes may operate in the subseafloor. These results expand the range of known geological settings that support biological activity to include submarine hydrothermal systems that are not dependent upon magmatic heat sources.

Archaea↗