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PubMed2001

Flow cytometry in oceanography 1989--1999: environmental challenges and research trends.

BACKGROUND: The present review is based on the identification of four major environmental crises that have been approached from a biological oceanographic viewpoint. These crises are the release of contaminants in near shore marine waters, the collapse of marine resources that were renewable until recently, the loss of biodiversity, and global climate change METHODS: The review examines the contribution of cytometry-based biological oceanography to the resolution of the four environmental crises. Using a database of 302 papers, flow cytometric (FCM) studies in biological oceanography over the 1989--1999 decade are examined. Future biological oceanographic applications of FCM are discussed. RESULTS: Most of the published FCM oceanographic studies focus on phytoplankton and bacterioplankton. Analysis of our 1989-1999 database shows the predominance of studies dedicated to phytoplankton (77%), followed by heterotrophic bacteria (21%). The latter progressively increased over the last decade, together with the improved understanding of the biogeochemical and trophic roles of marine bacteria. Most studies on these two microorganisms were conducted in vitro until 1996, after which the trend reversed in favor of in situ research. The most investigated areas were those with major international sampling efforts, related to the changing climate. Concerning environmental topics, 62% of papers on phytoplankton and bacterioplankton focused on the structure of microbial communities and fluxes (e.g., production, grazing); this provides the basis for biological oceanographic studies on resources and climate change. CONCLUSIONS: Future progress in the biological oceanographic use of FCM will likely fall into two categories, i.e., applications where FCM will be combined with the development of other methods and those where FCM will be the main analytical tool. It is expected that FCM and other cytometric approaches will improve the ability of biological oceanography to address the major environmental challenges that are confronting human societies.

Animals↗
PubMed2026

Phenacetin inhibited but acetaminophen stabilized partial nitrification/anammox system: Studies on microbial metabolism and resistance genes in biofilm and plastisphere.

Partial nitrification (PN) inhibitors, such as phenacetin (PNCT) and acetaminophen (APAP), ensure a stable nitrite supply for anaerobic ammonium oxidation (anammox). But the unknown impact of inhibitors on anammox limit the application of inhibitors. In addition to the biofilm carriers used in biological nitrogen removal systems, microplastics (MPs) (a type of emerging contaminants) are the common substrate for microbial colonization, even enriched resistance genes (RGs). This research compared the effects of 0.5, 1 and 5 mg/L PNCT or APAP on partial nitrification-anammox (PN/A) biofilm and plastisphere. 1 mg/L PNCT inhibited the nitrogen removal functional bacteria (Nitrosomonas, Candidatus Kuenenia, Candidatus Brocadia and Nitrospira), resulting in the sharp deteriorated performance of PN/A system. 5 mg/L PNCT inhibited multiple metabolism pathways, resulting in the absence of electrons and energy supply of microorganisms. 0.5-1 mg/L APAP maintained the stable operation of PN/A system. Nitrospira abundances declined from 2.8% to 1.1% after 0.5 mg/L APAP exposure. But 5 mg/L APAP inhibited the abundance of amoA and the production of extracellular polymeric substances, which caused the slight fluctuation of PN/A performance. PN inhibitors did not cause the sharp increase of most RGs in biofilm and water. However, MPs exhibited the huge capacity of enriching RGs, which should be removed. This study proposed that 0.5 mg/L of APAP was suitable for the PN/A system to control dosage for practical application.

Biofilms↗
PubMed2026

Shifts of antibiotic resistance genes across an estuarine meandering bend and dissemination risks to offshore oceans.

Meandering is a fundamental geomorphic feature of rivers that plays a critical role in regulating pollutant attenuation. To elucidate its impact on antibiotic resistance genes (ARGs) distribution in estuarine intertidal sediments, samples were collected from both the landward side (freshwater-dominated) and the seaward side (tide-dominated) of a meander bend during ebb and flood tides. The total relative abundance of ARGs was approximately 2.7 times higher on the landward side, peaking during the ebb tide. Microbial composition analysis showed that genera Acinetobacter and Pseudomonas were dominant at the landward sites, while halophilic genera such as Marinobacter and Exiguobacterium were abundant at the seaward sites. Further analysis of metagenome-assembled genomes (MAGs) demonstrated that the dominant landward genus Acinetobacter acted as a key host of ARGs, with two of four MAGs encoding more than ten ARGs. Notably, the total relative abundance of mobile genetic elements was high but consistent between sides and tidal cycles (p > 0.05). Given this high dissemination risk, we further forecasted the ARGs transfer scenarios to oceanic settings based on a set of offshore MAGs (n = 3626). Three ARGs, i.e., acrA, vanSL, and AAC(2')-Ia, were inferred to have transfer potential, supported by neighboring MGEs detected in marine microorganisms. Analysis of the genomes of predicted recipients in the SRA database confirmed the predicted mobilizations. Together, this study highlights that the meandering planform may serve as a significant barrier, attenuating the discharge of ARGs from terrestrial sources into the marine environment.

Estuaries↗
PubMedDate not supplied

[Distribution and diversity of conjugative plasmids among some multiple antibiotic resistant E.coli strains isolated from river waters].

In natural bacterial communities the microbial structure and functions are subjected to dynamic environmental and genetic adaptation. Plasmid-mediated horizontal genes transfer has a major impact on the adaptability of bacteria, exemplified by the interspecific and intergeneric transfer of antibioresistance genes in a variety of aquatic media. The high incidence of resistant bacteria has been documented for fresh waters, marine waters and chronically polluted waters. The aim of this study was to establish the distribution and diversity of plasmids and to study the transfer of plasmids harboring multiple antimicrobial-resistance determinants (R plasmids) belong to 12 multiple antibiotic resistant E. coli strains isolated from river waters. Antimicrobial resistance patterns were performed for aminoglycosides (gentamycin, kanamycin), beta-lactams (ampicillin), cephalosporins (ceftazidime and cefotaxime), tetracycline, nalidixic acid and chloramphenicol by disk diffusion method following NCCLS recommendations. Minimum inhibitory concentrations (MICs) were performed using dilution method in Mueller-Hinton broth with a 0.06-64 micrograms/ml concentration range for all antimicrobials and bacterial inoculum corresponding to 0.5 standard of the McFarland scale. For the data analysis NCCLS breakpoints for resistance and sensitivity were used. Bacterial plasmid isolation was performed by an alkaline lysis method. Genetic characterization was performed by agarose gel electrophoresis and spectrophotometric analysis. R-plasmid transfer frequencies were estimated by conjugation of drug-resistant E. coli strains used as donors with E. coli DH5 alpha F recipient marked with chromosomal resistance to nalidixic acid (Nal). The drug resistance markers possessed by a particular donor strain were sequentially used to screen for R+ transconjugants by incorporation the particular drug in the selective media. All E. coli strains are multiple antibiotic resistant, 65% of them being resistant to all 8 antibiotics tested. Plasmid profile analysis revealed the presence of several plasmids ranging from 3.8 kpb to more than 50 kpb. All aquatic R+ strains transferred two or more of their resistance markers to E. coli DH5 alpha F, transfer of resistance to ampicillin and tetracycline being the most frequent and having a frequency of 10(-4) or greater (expressed as transconjugants/donor). The phenotypic data shows the frequency and dynamic flow of multiple antibioresistant E. coli strains in aquatic media. Electrophoretic patterns analysis reflects the high incidence and diversity of plasmids in aquatic E. coli strains. Plasmid-harboring E. coli strains transferred antibiotic resistance and, hence, possessed conjugative R plasmids. Of these, 80% transferred drug resistance at a frequency of about 10(-4).

Anti-Bacterial Agents↗
PubMedDate not supplied

[Dynamics of organic matter decomposition and microflora composition of forest litter in artificial biogeocenoses].

The dynamics of litter stock, microbial biomass, and composition and structure of microbial communities, were studied in the course of soil organic matter transformation during vegetation season. The dynamics of litter stock in coniferous and deciduous forests proved to correlate with the biomass and total abundance of microorganisms, particularly, with the proportion of microfungi in the microbial community.

Biodegradation, Environmental↗
PubMed2000

Heterogeneity in biofilms.

Biofilms, accumulations of microorganisms at interfaces, have been described for every aqueous system supporting life. The structure of these microbial communities ranges from monolayers of scattered single cells to thick, mucous structures of macroscopic dimensions (microbial mats; algal-microbial associations; trickling filter biofilms). During recent years the structure of biofilms from many different environments has been documented and evaluated by use of a broad variety of microscopic, physico-chemical and molecular biological techniques, revealing a generally complex 3D structure. Parallel to these investigations more and more complex mathematical models and simulations were developed to explain the development, structures, and interactions of biofilms. The forces determining the spatial structure of biofilms, including microcolonies, extracellular polymeric substances (EPS), and channels, are still the subject of controversy. To achieve conclusive explanations for the structures observed in biofilms the cooperation of both fields of investigation, modelling and experimental research, is necessary. The expanding field of molecular techniques not only allows more and more detailed documentation of the spatial distribution of species, but also of functional activities of single cells in their biofilm environment. These new methods will certainly reveal new insights in the mechanisms involved in the developmental processes involved in the formation and behavior of biofilms.

Bacteria↗
PubMed2006

Technology development to explore the relationship between oral health and the oral microbial community.

The human oral cavity contains a complex microbial community that, until recently, has not been well characterized. Studies using molecular tools have begun to enumerate and quantify the species residing in various niches of the oral cavity; yet, virtually every study has revealed additional new species, and little is known about the structural dynamics of the oral microbial community or how it changes with disease. Current estimates of bacterial diversity in the oral cavity range up to 700 species, although in any single individual this number is much lower. Oral microbes are responsible for common chronic diseases and are suggested to be sentinels of systemic human diseases. Microarrays are now being used to study oral microbiota in a systematic and robust manner. Although this technology is still relatively young, improvements have been made in all aspects of the technology, including advances that provide better discrimination between perfect-match hybridizations from non-specific (and closely-related) hybridizations. This review addresses a core technology using gel-based microarrays and the initial integration of this technology into a single device needed for system-wide studies of complex microbial community structure and for the development of oral diagnostic devices.

Journal Article↗
PubMed2006

[Application of modern molecular biology techniques to study micro-ecosystem in the rumen].

The microbial community inhabiting in the rumen is characterized by its high population density, wide diversity and interactive complexity. However, until recently our knowledge of rumen microbiology was primarily based on classical culture based techniques (isolation, enumeration and nutritional characterization) which probably only account for 10% to 20% of the rumen microbial population. Modem molecular biology techniques provide effective methods to study the micro-ecosystem in the rumen. The use of molecular techniques based on nucleic acid probes is likely to revolutionize the approach to microbial ecology in the rumen and provide, not simply a refinement or increased understanding but a complete description of rumen community for the first time. Modem molecular techniques based on sequence comparisons of nucleic acids may be used to explore molecular characterization and provide a classification scheme which predicts natural evolutionary relationships. Genetic fingerprinting techniques that provide a pattern or profile of genetic diversity have been applied in a variety of environmental studies for the analysis of microbial communities. Whole-cell hybridization is a powerful technique which may be used to study the structure and function of microbial communities in situ and describe the expression of key enzymes. Real-time quantitative PCR technique may be conducted to accurately quantify the target microorganisms in the rumen. Development of these procedures and techniques will result in greater insights into community structure and activity of rumen microbial communities in relation to functional interactions, spatial and temporal relationships between different microorganisms and between microorganisms and feed particles. The successful development and application of these methods promise to provide the first opportunity to link distribution and identity of rumen microbes in their natural environment with their genetic potential and in situ activities.

Animals↗
PubMed2006

Bacterial community structure, compartmentalization and activity in a microbial fuel cell.

AIMS: To characterize bacterial populations and their activities within a microbial fuel cell (MFC), using cultivation-independent and cultivation approaches. METHODS AND RESULTS: Electron microscopic observations showed that the fuel cell electrode had a microbial biofilm attached to its surface with loosely associated microbial clumps. Bacterial 16S rRNA gene libraries were constructed and analysed from each of four compartments within the fuel cell: the planktonic community; the membrane biofilm; bacterial clumps (BC) and the anode biofilm. Results showed that the bacterial community structure varied significantly between these compartments. It was observed that Gammaproteobacteria phylotypes were present at higher numbers within libraries from the BC and electrode biofilm compared with other parts of the fuel cell. Community structure of the MFC determined by analyses of bacterial 16S rRNA gene libraries and anaerobic cultivation showed excellent agreement with community profiles from denaturing gradient gel electrophoresis (DGGE) analysis. CONCLUSIONS: Members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and other Gammaproteobacteria with Fe(III)-reducing and electrochemical activity had a significant potential for energy generation in this system. SIGNIFICANCE AND IMPACT OF THE STUDY: This study has shown that electrochemically active bacteria can be enriched using an electrochemical fuel cell.

Anaerobiosis↗
PubMed2001

Functional and structural response of a cellulose-degrading methanogenic microbial community to multiple aeration stress at two different temperatures.

Two cellulose-fermenting methanogenic enrichment cultures originating from rice soil, one at 15 degrees C with Methanosaeta and the other at 30 degrees C with Methanosarcina as the dominant acetoclastic methanogen, both degraded cellulose anaerobically via propionate, acetate and H2 to CH4. The degradation was a two-stage process, with CH4 production mainly from H2/CO2 and accumulation of acetate and propionate during the first, and methanogenic consumption of acetate during the second stage. Aeration stress of 12, 24, 36 and 76 h duration was applied to these microbial communities during both stages of cellulose degradation. The longer the aeration stress, the stronger the inhibition of CH4 production at both 30 degrees C and 15 degrees C. The 72 h stressed culture at 30 degrees C did not fully recover. Aeration stress at 30 degrees C exerted a more pronounced effect, but lasted for a shorter time than that at 15 degrees C. The aeration stress was especially effective during the second stage of fermentation, when consumption of acetate (and to a lesser extent propionate) was also increasingly inhibited as the duration of the stress increased. The patterns of CH4 production and metabolite accumulation were consistent with changes observed in the methanogenic archaeal community structure. Fluorescence in situ hybridization showed that the total microbial community at the beginning consisted of about 4% and 10% archaea, which increased to about 50% and 30% during the second stage of cellulose degradation at 30 degrees C and 15 degrees C respectively. Methanosarcina and Methanosaeta species became the dominant archaea at 30 degrees C and 15 degrees C respectively. The first round of aeration stress mainly reduced the non-Methanosarcina archaea (30 degrees C) and the non-Methanosaeta archaea (15 degrees C). Aeration stress also retarded the growth of Methanosarcina and Methanosaeta at 30 degrees C and 15 degrees C respectively. The longer the stress, the lower was the percentage of Methanosarcina cells to total microbial cells after the first stress at 30 degrees C. A later aeration stress decreased the population of Methanosarcina (at 30 degrees C) in relation to the duration of stress, so that non-Methanosarcina archaea became dominant. Hence, aeration stress affected the acetotrophic methanogens more than the hydrogenotrophic ones, thus explaining the metabolism of the intermediates of cellulose degradation under the different incubation conditions.

Air↗
PubMed2003

The microbiology of biological phosphorus removal in activated sludge systems.

Activated sludge systems are designed and operated globally to remove phosphorus microbiologically, a process called enhanced biological phosphorus removal (EBPR). Yet little is still known about the ecology of EBPR processes, the microbes involved, their functions there and the possible reasons why they often perform unreliably. The application of rRNA-based methods to analyze EBPR community structure has changed dramatically our understanding of the microbial populations responsible for EBPR, but many substantial gaps in our knowledge of the population dynamics of EBPR and its underlying mechanisms remain. This review critically examines what we once thought we knew about the microbial ecology of EBPR, what we think we now know, and what still needs to be elucidated before these processes can be operated and controlled more reliably than is currently possible. It looks at the history of EBPR, the currently available biochemical models, the structure of the microbial communities found in EBPR systems, possible identities of the bacteria responsible, and the evidence why these systems might operate suboptimally. The review stresses the need to extend what have been predominantly laboratory-based studies to full-scale operating plants. It aims to encourage microbiologists and process engineers to collaborate more closely and to bring an interdisciplinary approach to bear on this complex ecosystem.

Aerobiosis↗
PubMed2003

Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus).

The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.

Bacteria↗
PubMed2001

Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment.

Soil structure depends on the association between mineral soil particles (sand, silt, and clay) and organic matter, in which aggregates of different size and stability are formed. Although the chemistry of organic materials, total microbial biomass, and different enzyme activities in different soil particle size fractions have been well studied, little information is available on the structure of microbial populations in microhabitats. In this study, topsoil samples of different fertilizer treatments of a long-term field experiment were analyzed. Size fractions of 200 to 63 microm (fine sand fraction), 63 to 2 microm (silt fraction), and 2 to 0.1 microm (clay fraction) were obtained by a combination of low-energy sonication, wet sieving, and repeated centrifugation. Terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes were used to compare bacterial community structures in different particle size fractions. The microbial community structure was significantly affected by particle size, yielding higher diversity of microbes in small size fractions than in coarse size fractions. The higher biomass previously found in silt and clay fractions could be attributed to higher diversity rather than to better colonization of particular species. Low nutrient availability, protozoan grazing, and competition with fungal organisms may have been responsible for reduced diversities in larger size fractions. Furthermore, larger particle sizes were dominated by alpha-Proteobacteria, whereas high abundance and diversity of bacteria belonging to the Holophaga/Acidobacterium division were found in smaller size fractions. Although very contrasting organic amendments (green manure, animal manure, sewage sludge, and peat) were examined, our results demonstrated that the bacterial community structure was affected to a greater extent by the particle size fraction than by the kind of fertilizer applied. Therefore, our results demonstrate specific microbe-particle associations that are affected to only a small extent by external factors.

Bacteria↗
PubMed2006

Protein extraction and fingerprinting optimization of bacterial communities in natural environment.

Recent development in molecular approaches allows access to genetic structure and diversity of indigenous microbial communities. In contrast, the functional analysis of microorganisms in their environment is still hampered by methodological limitations. Analysis of total proteins expressed at the whole community level (metaproteome) has been proposed to characterize the functional structure of microbial communities in their environment. However, developments are still required to perform such analysis. Our aim was to optimize methods to extract and characterize metaproteome of indigenous microbial communities. Experiments were first conducted in monoxenic bacterial cultures, and various methods were examined to define a procedure of protein extraction ensuring an efficient recovery regardless of the taxonomic affiliation of the cells. These developments were next applied to characterize the metaproteome from indigenous bacterial communities in freshwater samples. Bacterial cells were recovered from water using a high-speed density gradient centrifugation method before protein extraction and fingerprinting. The reactivity and sensitivity of this metaproteomic approach were tested by analyzing the variations of protein fingerprints according to perturbations (cadmium or mercury contamination). The genetic structure of the corresponding communities was also characterized by automated ribosomal spacer analysis (ARISA) DNA fingerprinting. Both protein and DNA fingerprints were statistically analyzed. Results obtained showed that the method developed for protein recovery and fingerprinting was efficient, sensitive, and reproducible. Both the functional and genetic structures of the freshwater bacterial community were complex and varied with perturbations. These variations occurred at both population and protein expression levels and were specific to the perturbation applied.

Bacteria↗
PubMed2026

Microbial succession and assembly shaped by sulfur, spatial partitioning, and water flow in a volcanic acidic river of northern Patagonia.

Extreme acidic environments represent natural laboratories for investigating the mechanisms of microbial community assembly, yet the ecological processes structuring these communities remain incompletely understood. Here, we investigate how spatial partitioning, hydrodynamics, and colonization history shape microbial succession in a unique sulfur-rich, acidic river of volcanic origin in northern Patagonia. We combined 16S rRNA gene profiling and shotgun metagenomics with a multi-scale experimental framework encompassing water column fractionation and colonization assays under native and controlled conditions. Microbial diversity was strongly influenced by spatial fractionation, with free-living communities exhibiting higher richness and temporal variability than particle-associated assemblages. Water flow modulated community structure, increasing evenness in free-living fractions under high-flow conditions, but had limited impact on particle-attached communities. Colonization of sulfur-beads followed a structured successional trajectory, with autotrophic sulfur oxidizers dominating early stages and heterotrophs adapted to biofilm lifestyles increasing over time. Ex situ recolonization assays revealed strong priority effects, with initial colonizers determining successional trajectories. Turnover analyses revealed that the balance among stochastic and deterministic assembly processes shifted across communities with pronounced stochasticity in the water column and flow-dependent effects in free-living communities, while biofilm associated communities on sulfur-beads exhibited stronger contribution of deterministic selection. These ecological patterns were mirrored by functional differentiation, with gene enrichment analyses revealing adaptive signatures of substrate attachment and resource acquisition. By integrating fine-scale environmental variation with colonization dynamics, this study reveals how microscale habitat structure and temporal fluxes jointly modulate microbial community assembly rules, offering a nuanced framework to dissect ecological processes in extreme systems.

Sulfur↗
PubMed2006

Spatial variability of isoproturon mineralizing activity within an agricultural field: geostatistical analysis of simple physicochemical and microbiological soil parameters.

We assessed the spatial variability of isoproturon mineralization in relation to that of physicochemical and biological parameters in fifty soil samples regularly collected along a sampling grid delimited across a 0.36 ha field plot (40 x 90 m). Only faint relationships were observed between isoproturon mineralization and the soil pH, microbial C biomass, and organic nitrogen. Considerable spatial variability was observed for six of the nine parameters tested (isoproturon mineralization rates, organic nitrogen, genetic structure of the microbial communities, soil pH, microbial biomass and equivalent humidity). The map of isoproturon mineralization rates distribution was similar to that of soil pH, microbial biomass, and organic nitrogen but different from those of structure of the microbial communities and equivalent humidity. Geostatistics revealed that the spatial heterogeneity in the rate of degradation of isoproturon corresponded to that of soil pH and microbial biomass.

Agriculture↗
PubMed2024

Environmental stress mediates groundwater microbial community assembly.

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

Phylogeny↗