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PubMed2001

Brines in seepage channels as eluants for subsurface relict biomolecules on Mars?

Water, vital for life, not only maintains the integrity of structural and metabolic biomolecules, it also transports them in solution or colloidal suspension. Any flow of water through a dormant or fossilized microbial community elutes molecules that are potentially recognizable as biomarkers. We hypothesize that the surface seepage channels emanating from crater walls and cliffs in Mars Orbiter Camera images results from fluvial erosion of the regolith as low-temperature hypersaline brines. We propose that, if such flows passed through extensive subsurface catchments containing buried and fossilized remains of microbial communities from the wet Hesperian period of early Mars (approximately 3.5 Ga ago), they would have eluted and concentrated relict biomolecules and delivered them to the surface. Life-supporting low-temperature hypersaline brines in Antarctic desert habitats provide a terrestrial analog for such a scenario. As in the Antarctic, salts would likely have accumulated in water-filled depressions on Mars by seasonal influx and evaporation. Liquid water in the Antarctic cold desert analogs occurs at -80 degrees C in the interstices of shallow hypersaline soils and at -50 degrees C in salt-saturated ponds. Similarly, hypersaline brines on Mars could have freezing points depressed below -50 degrees C. The presence of hypersaline brines on Mars would have extended the amount of time during which life might have evolved. Phototrophic communities are especially important for the search for life because the distinctive structures and longevity of their pigments make excellent biomarkers. The surface seepage channels are therefore not only of geomorphological significance, but also provide potential repositories for biomolecules that could be accessed by landers.

Extraterrestrial Environment↗

PubMed2003

Microbial impacts on plant-herbivore interactions: the indirect effects of a birch pathogen on a birch aphid.

The role of indirect interactions in structuring communities is becoming increasingly recognised. Plant fungi can bring about changes in plant chemistry which may affect insect herbivores that share the same plant, and hence the two may interact indirectly. This study investigated the indirect effects of a fungal pathogen ( Marssonina betulae) of silver birch ( Betula pendula) on an aphid ( Euceraphis betulae), and the processes underpinning the interaction. There was a strong positive association between natural populations of the aphid and leaves bearing high fungal infection. In choice tests, significantly more aphids settled on leaves inoculated with the fungus than on asymptomatic leaves. Individual aphids reared on inoculated leaves were heavier, possessed longer hind tibiae and displayed enhanced embryo development compared with aphids reared on asymptomatic leaves; population growth rate was also positively correlated with fungal infection when groups of aphids were reared on inoculated branches. Changes in leaf chemistry were associated with fungal infection with inoculated leaves containing higher concentrations of free-amino acids. This may reflect a plant-initiated response to fungal attack in which free amino acids from the degradation of mesophyll cells are translocated out of infected leaves via the phloem. These changes in plant chemistry are similar to those occurring during leaf senescence, and are proposed as the mechanistic basis for the positive interaction between the fungus and aphid.

Amino Acids↗

PubMed2002

Microbial diversity and complexity in hypersaline environments: a preliminary assessment.

The microbial communities in solar salterns and a soda lake have been characterized using two techniques: BIOLOG, to estimate the metabolic potential, and amplicon length heterogeneity analysis, to estimate the molecular diversity of these communities. Both techniques demonstrated that the halophilic Bacteria and halophilic Archaea populations in the Eilat, Israel saltern are dynamic communities with extensive metabolic potentials and changing community structures. Halophilic Bacteria were detected in Mono Lake and the lower salinity ponds at the Shark Bay saltern in Western Australia, except when the crystallizer samples were stressed by exposure to Acid Green Dye #9899. At Shark Bay, halophilic Archaea were found only in the crystallizer samples. These data confirm both the metabolic diversity and the phylogenetic complexity of the microbial communities and assert the need to develop more versatile media for the cultivation of the diversity of bacteria in hypersaline environments.

Archaea↗

PubMed2002

Modelling of activated sludge processes with structured biomass.

Bacterial communities when subjected to feast-famine conditions as occurring in many wastewater treatment systems store substrates as reserve polymers. Including storage polymers in a description of microbial growth processes makes important the choice of kinetic relations. Presently there is no sound description for the diversion of substrate towards biomass growth or substrate storage. Based on observations with pure cultures and mixed cultures growing under dynamic conditions a model is proposed to describe such behaviour. This description is based on the observation that bacteria in order to grow fast have to induce a high level of RNA and proteins in order to allow fast growth. We assume that this protein synthesising system is only induced in the presence of external substrates. Based on this assumption a model structure is proposed and evaluated. It seems that this model can predict the turnover of PHA in the cells correctly, and describes well the overall behaviour mixed culture SBR systems. However especially the growth rate in the famine phase seems to be overestimated. The model defined here is a contribution to a further development of mechanistically based models for activated sludge processes.

Biomass↗

PubMed1996

Development of a steady-state oral microbial biofilm community using the constant-depth film fermenter.

The complexity of biofilm communities like dental plaque suggests that laboratory model biofilm growth systems may help to understand their structure and function. This study describes the use of a constant-depth film fermenter (CDFF) to investigate biofilm formation by a nine-membered community of oral bacteria. The community was grown to steady state in a chemostat incubated anaerobically. The chemostat output was fed into the CDFF incubated aerobically. Viable counts for each species from the chemostat and the CDFF at steady state showed major differences; however, all nine organisms were present under both conditions. There was evidence of succession during biofilm formation with obligately anaerobic species only establishing after several days. A steady-state biofilm community was achieved which remained stable over time. Electron microscopy showed evidence of spatial differentiation with what appeared to be Neisseria subflava dominant near the upper surface and Fusobacterium nucleatum largely confined to the middle portion.

Bacteria, Anaerobic↗

PubMed1999

Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis.

16S rDNA clone libraries were analysed to investigate the microbial diversity in marine sediments from Sagami Bay (stations SA, water depth of 1159 m, and SB, 1516 m) and Tokyo Bay (station TK, 43 m). A total of 197 clones was examined by amplified rDNA restriction analysis (ARDRA) using three four-base-specific restriction enzymes (Hhal, Rsal and Haelll). In SA, 57 RFLP types were detected from 77 clones. In SB, 17 RFLP types were detected from 62 clones. In TK, 21 RFLP types were detected from 58 clones. The genotypic diversity among the three sampling sites was 0.958, 0.636 and 0.821, respectively, indicating that the microbial diversity of SA was higher than at the other two stations. At SA, the most abundant RFLP type constituted 10% of all clones. The samples from SB and TK had dominant RFLP types which constituted 60% and 38% of the total clone libraries, respectively. The community structure of SA included many single-type clones, which were found only once in the clone libraries. This structure contrasted with that of the other two stations. Thirty-seven clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the microbial diversity in the clone libraries. No clones were identical to any of the known 165 rRNA sequences or to each other. All sequences had >84.8% similarity to rDNA sequences retrieved from the DNA databases. Sequenced clones fell into five major lineages of the domain Bacteria: the gamma, delta and epsilon Proteobacteria, Gram-positive bacteria and the division Verrucomicrobia. At SA, the Verrucomicrobia and the three subclasses of the Proteobacteria were found. Most clone sequences belonged to the gamma Proteobacteria. The high-GC Gram-positive bacteria and the gamma subclass of the Proteobacteria were common at both SB and TK. Although the depths of SB and TK were very different, the community diversity inferred from ARDRA and the taxonomic position of the dominant clones were similar. All clones belonging to the highGC Gram-positive bacteria collected from both SB and TK fell into the same cluster and are regarded as members of an unknown actinomycete group. The clone compositions were different at each sampling site, and clones of the gamma Proteobacteria and high-GC Gram-positive bacteria were dominant.

Bacteria↗

PubMed2005

A survey of ammonia-assimilating micro-organisms in cattle manure composting.

AIMS: To evaluate the ammonia-assimilating abilities of micro-organisms isolated from cattle manure composting processes and to determine the distribution of cultivable species of ammonia-assimilating micro-organisms in microbial communities during the composting processes. METHODS AND RESULTS: Compost samples were collected from four stages of treatment. Trypto soya agar was used for the isolation of ammonia-assimilating aerobes. Many of the isolates showed high ammonia-assimilating ability in a medium containing basal components and a compost extract. Partial 16S ribosomal DNA sequencing showed that the cultivable species of highly efficient ammonia-assimilating isolates changed during the composting process. The community structure of micro-organisms and actinomycetes was analysed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Two species of actinomycetes identified by PCR-DGGE coincided with those found among the cultured isolates. CONCLUSIONS: Ammonia-assimilating micro-organisms obtained by the cultivation method were not predominant in the microbial community during the composting process: however certain cultured actinomycetes were members of predominant species in the actinomycetes community. SIGNIFICANCE AND IMPACT OF THE STUDY: Ammonia assimilation by micro-organisms is one of the important mechanisms for ammonia retention in the composting process. Cultivable actinomycetes are a means for preventing ammonia emission from the composting process.

Actinomyces↗

PubMed1967

Inhibition of the lysis of fungi by melanins.

Evidence is presented that the resistance of Aspergillus nidulans hyphae to lysis by a beta-(1-->3) glucanase-chitinase mixture results from the presence of melanin in the fungal walls. The resistance of the walls to digestion was directly correlated with the melanin content of the mycelium. A melanin-less mutant of A. nidulans was highly susceptible to hydrolysis by the enzyme mixture. Preincubation of a synthetic melanin with the glucanase, chitinase, and a protease, before addition of the substrate, resulted in a marked inhibition of the rate of substrate hydrolysis. Melanin also appeared to combine with and protect at least certain substrates from decomposition, as indicated by the direct relationship between the extent of inhibition of casein hydrolysis by a bacterial protease and the length of time the protein was incubated with the melanin prior to addition of the enzyme. Melanin was found to be highly resistant to microbial degradation, a likely requirement for the polyaromatic to be effective in protecting fungal structures from lysis or decomposition by natural communities of microorganisms.

Aspergillus↗

PubMed2026

Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.

BACKGROUND: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood. RESULTS: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103 days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6 h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24 h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24 h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained. CONCLUSIONS: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.

Biofilms↗

PubMed1996

Study of the microbial dynamics in the root environment of closed, hydroponic cultivation systems for tomato using phospholipid fatty acid profiles.

A more basic understanding of the microbial dynamics of closed, hydroponic cultivation systems is needed. We therefore initiated a study of the microbial community inhabiting the root environment, using phospholipid fatty acid (PLFA) profiles, and started to examine whether changes in the microbial population structure would result from the introduction of selected isolates of plant growth-promoting rhizobacteria (PGPR). Tomato were cultured in deep-flow systems with circulating nutrient solution. Bacteria were sampled from tomato roots at three locations, longitudinally, in the gutters of a control system and in two systems inoculated with PGPR. In the beginning of the gutters the PLFA profiles were similar in all systems, whereas the profiles differed in the gutter ends (following the direction of flow). In the control system, and in a treatment inoculated with two Gram-negative and one Gram-positive PGPR strain, the relative proportion of PLFAs characteristic to Gram-positive bacteria was highest at the end of the gutter. In a treatment inoculated only with a Gram-negative PGPR strain, the relative proportion of PLFAs characteristic of Gram-negative bacteria was highest at the end of the gutter. The results indicate a complex situation with different micro-environments distributed along the root mat. It can also be concluded that PLFA profiles may be useful tools in the study of the microbiology of closed hydroponic plant cultivation systems.

Cluster Analysis↗

PubMed2000

Horizontal Distribution Patterns of Testate Amoebae (Protozoa) in a Sphagnum magellanicum Carpet.

The distribution of soil microorganisms is generally believed to be patchy and to reflect habitat heterogeneity. Despite this general rule, the amount of existing data on species distribution patterns is scarce. Testate amoebae (Protozoa; Rhizopoda) are an important component of soil microbial communities and are increasingly used in ecological and paleoecological studies of Sphagnum-dominated peatlands, but data on the spatial structure of communities are completely lacking. This is an important aspect since quantitative models used for paleoecological reconstruction and monitoring are based on species assemblages. We explored the distribution patterns of testate amoebae distribution in a macroscopically homogeneous Sphagnum carpet, down to a scale of several centimeters. Distributions maps of the species and spatially constrained sample groups were produced. Multivariate and individual spatial autocorrelations were calculated. The importance of spatial structure was quantified by canonical correspondence analysis. Our ultimate goal is to find the finest resolution of environmental monitoring using testate amoebae. The distribution patterns differed among species, resulting in a complex spatial structure of the species assemblage in a whole. Spatial structure accounted for 36% of the total variation of species abundance in a canonical correspondence analysis constrained by spatial variables. This structure was partly correlated to altitude (microtopography) at a very fine scale. These results confirmed the existence of significant broad- and fine-scale spatial structures within testate amoebae communities that could in part be interpreted as effects of ecological gradients. This shows that, on a surface area of 0.25 m(2), ecological conditions which look uniform from a macroscopic point of view are not perceived as such by Sphagnum-inhabiting organisms. Therefore, testate amoebae could prove very useful to monitor fine-scale ecological processes or disturbances. Studies of the species' spatial distribution patterns in combination with autoecological studies are needed and should be included in the toolbox of biomonitoring itself.

Journal Article↗

PubMed2026

Lifestyle Differentiation Among Marine Denitrifying Microorganisms.

Microorganisms carrying out denitrification in marine anoxic zones drive bioavailable nitrogen loss. Sequencing datasets have demonstrated the modularity of denitrification, with most populations having the genetic capability for only a subset of the pathway (NO3-➔NO2-➔NO➔N2O➔N2). Although previous work provided ecological explanations for this diversity among the functional modules, large trait variations exist within each functional module, and this within-module diversity and its biogeochemical implications remain unexplored. Here, we combine genomic data and modeling to explore how metabolic "lifestyle" strategies influence denitrifier community structure. We build a comprehensive genomic database of marine denitrifiers, and identify lifestyle differentiation among denitrifier functional groups. We then extend a mathematical ecosystem model by resolving two microbial functional types for each module representing a metabolic trade-off: a copiotroph, optimized for fast growth, and an oligotroph, optimized for high nutrient affinity. In the model, as the supply of organic matter relative to nitrate increases, the degree of copiotrophy among the community increases and then decreases. This suggests that oligotrophs are associated with either organic-matter- or nitrate-limiting conditions, whereas copiotrophic lifestyles are associated with an intermediate regime. Our model further associates NO2- reducers with oligotrophy and NO3- reducers with copiotrophy, particularly those producing greenhouse gas nitrous oxide (N2O), linking N2O production to substrate-replete conditions, which is consistent with our genome-based lifestyle estimates. Results provide insight into denitrifier ecological niches and thus the biogeochemical conditions that are associated with the production of intermediates, such as N2O, improving our understanding of how nitrogen cycling will change in a warming ocean.

Marine denitrifiers↗

PubMed2002

Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer.

Microbial sulfate reduction is an important metabolic activity in petroleum hydrocarbon (PHC)-contaminated aquifers. We quantified carbon source-enhanced microbial SO(4)(2-) reduction in a PHC-contaminated aquifer by using single-well push-pull tests and related the consumption of sulfate and added carbon sources to the presence of certain genera of sulfate-reducing bacteria (SRB). We also used molecular methods to assess suspended SRB diversity. In four consecutive tests, we injected anoxic test solutions (1,000 liters) containing bromide as a conservative tracer, sulfate, and either propionate, butyrate, lactate, or acetate as reactants into an existing monitoring well. After an initial incubation period, 1,000 liters of test solution-groundwater mixture was extracted from the same well. Average total test duration was 71 h. We measured concentrations of bromide, sulfate, and carbon sources in native groundwater as well as in injection and extraction phase samples and characterized the SRB population by using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Enhanced sulfate reduction concomitant with carbon source degradation was observed in all tests. Computed first-order rate coefficients ranged from 0.19 to 0.32 day(-1) for sulfate reduction and from 0.13 to 0.60 day(-1) for carbon source degradation. Sulfur isotope fractionation in unconsumed sulfate indicated that sulfate reduction was microbially mediated. Enhancement of sulfate reduction due to carbon source additions in all tests and variability of rate coefficients suggested the presence of specific SRB genera and a high diversity of SRB. We confirmed this by using FISH and DGGE. A large fraction of suspended bacteria hybridized with SRB-targeting probes SRB385 plus SRB385-Db (11 to 24% of total cells). FISH results showed that the activity of these bacteria was enhanced by addition of sulfate and carbon sources during push-pull tests. However, DGGE profiles indicated that the bacterial community structure of the dominant species did not change during the tests. Thus, the combination of push-pull tests with molecular methods provided valuable insights into microbial processes, activities, and diversity in the sulfate-reducing zone of a PHC-contaminated aquifer.

Colony Count, Microbial↗

PubMed2004

Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms.

A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved (Nardus stricta, Agrostis capillaris, Festuca ovina and F. rubra) and fertilized, improved (Holcus lanatus, Lolium perenne and Trifolium repens) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects.

Analysis of Variance↗

PubMed2005

Simazine biodegradation in soil: analysis of bacterial community structure by in situ hybridization.

Pesticide and nitrate contamination of soil and groundwater from agriculture is an environmental and public health concern worldwide. Simazine, 6-chloro-N2,N4-diethyl-1,3,5-triazine-2,4-diamine, is a triazine herbicide used in agriculture for selective weed control with several types of crops and it is frequently applied to soils receiving N-fertilizers. Degradation experiments were performed in the laboratory to assess whether the biodegradation of simazine in soil may be influenced by the presence of urea. Simazine degradation rates under different experimental conditions (presence/absence of urea, microbiologically active/sterilized soil) were assessed together with the formation, degradation and transformation of its main metabolites in soil. Simazine degradation was affected by the presence of urea, in terms both of a smaller half-life (t(1/2)) and of a higher amount of desethyl-simazine formed. The soil bacterial community was also studied. Microbial abundances were determined by epifluorescence direct counting. Moreover in situ hybridization with rRNA-targeted fluorescent oligonucleotide probes was used to analyze the bacterial community structure. Fluorescent in situ hybridization (FISH) was used to detect specific groups of bacteria such as the alpha,beta,gamma-subdivisions of Proteobacteria, Gram-positive bacteria with a high G + C DNA content, Planctomycetes, Betaproteobacterial ammonia-oxidizing bacteria and nitrifying bacteria. The presence of the herbicide and/or urea affected the bacterial community structure, showing that FISH is a valuable tool for determining the response of bacterial populations to different environmental conditions.

Bacteria↗

PubMed2005

In situ measurements of metabolite fluxes: microinjection of radiotracers into insect guts and other small compartments.

In microbial ecology, it is of great interest to determine metabolic activities under in situ conditions, i.e., without disturbing the structure of the community and the spatial arrangement of individual populations by experimental manipulation. Microinjection of radiotracers and subsequent analysis using the isotope dilution technique has proven to be a powerful method to measure metabolic fluxes in small biological systems, e.g., the intestinal tract of termites. The large variety of commercially available radiolabeled substrates and the identification and quantitation of radiolabeled products by chromatographic methods allow for investigation of the complete metabolic network in a given system.

Animals↗

PubMed2002

Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria.

Predation is a major mortality factor of planktonic bacteria and an important shaping force for the phenotypic and taxonomic structure of bacterial communities. In this paper we: (1) summarise current knowledge on bacterial phenotypic properties which affect their vulnerability towards grazers, and (2) review experimental evidence demonstrating that this phenotypic heterogeneity results in shifts of bacterial community composition during enhanced protist grazing pressure. Size-structured interactions are especially important in planktonic systems and bacterial cell size influences the mortality rate and the type of grazer to which bacteria are most susceptible. When protists are the major bacterivores, both very small and large bacterial cells gain some size refuge. Recent studies have revealed that also various non-morphological traits such as motility, physicochemical surface characters and toxicity affect bacterial vulnerability and protist feeding success. These properties are effective at different stages during the feeding process of interception feeding flagellates (encounter, capture, ingestion, digestion). Grazing-resistant bacteria in natural communities can account for a substantial portion of the total bacterial biomass at least in more productive aquatic systems. In field and laboratory experiments it has been demonstrated that increased protozoan grazing results in shifts in the phenotypic and genotypic composition of the bacterial assemblage. The importance of this shaping force for the bacterial community structure depends, however, on the overall food web structure, especially on the composition of the metazooplankton. Whereas the structuring impact of bacterial grazers is well documented, relatively little is known about how grazing-mediated changes in bacterial communities influence microbially mediated processes and biogeochemically important transformations.

Animals↗

PubMed2004

Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?

The gut contains our largest collection of resident microorganisms. One obvious question is how microbial communities establish and maintain themselves within a perfused intestine. The answers, which may come in part from observations made by environmental engineers and glycobiologists, have important implications for immunologists who wish to understand how indigenous microbial communities are accommodated. Here we propose that the mucus gel layer overlying the intestinal epithelium is a key contributor to the structural and functional stability of this microbiota and its tolerance by the host.

Animals↗