Functional Groups Of Microorganisms Research Articles

Grupos Funcionales de Microorganismos en Suelos de Páramo Perturbados por Incendios Forestales

El ecosistema estratégico del páramo de Rabanal (Boyacá - Colombia) fue afectado por incendios forestales que arrasaron 2000 hectáreas de vegetación nativa y las especies de fauna asociadas. Debido a esta problemática y a la reconocida importancia de los grupos funcionales de microorganismos como indicadores de calidad, se realizó un diagnóstico microbiológico de suelos para evaluar el efecto de la quema sobre estos grupos cultivables de microorganismos. También se efectuó el mismo diagnóstico en un suelo sin perturbar de la misma zona que se asumiría como control. Fueron evaluadas algunas poblaciones de bacterias cultivables implicadas en los ciclos del C, N y P por el método de recuento en placa estándar utilizando medios de cultivo selectivos. En general, las poblaciones microbianas cultivables nativas implicadas en el ciclado de nutrientes registraron valores de Log UFC/g de suelo similares en los dos tipos de suelos en estudio (p>0,05) a excepción de las poblaciones de bacterias proteolíticas y de bacterias solubilizadoras de fosfato. Las correlaciones lineales entre los diferentes grupos de microorganismos para los dos tipos de suelos evaluados resultaron en su mayoría estadísticamente signifi cativas y muestran interacciones positivas entre los grupos de microorganismos evaluados, lo que indicaría que las poblaciones estarían actuando sinérgicamente posibilitando procesos de cometabolismo, lo que conduciría a favorecer la recuperación del suelo degradado.

Molecular analysis of bacterial diversity in mudflats along the salinity gradient of an acidified tropical Bornean estuary (South East Asia).

BackgroundThe Brunei River and Bay estuarine system (BES) in the northwest of Borneo is acidic and highly turbid. The system supports extensive intertidal mudflats and presents a potentially steep salinity and pH gradient along its length (45 km). Temporal variation in physical parameters is observed diurnally due to seawater flux during tidal forcing, and stochastically due to elevated freshwater inflow after rains, resulting in a salinity range between 0 and 34 psu. High velocity freshwater run-off from acid sulphate formations during monsoon seasons results in highly variable and acidic conditions (pH 4) at the upper reaches of the BES, whereas the pH is relatively stable (pH 8) at the seaward extremes, due to mixing with seawater from the South China Sea. At their surfaces, the BES mudflats present microbial ecosystems driven by oxygenic phototrophs. To study the effect of various physical parameters on the bacterial diversity of the BES mudflats, surface samples were collected from six sites stretching over 40 km for molecular and phylogentic analysis.ResultsThe bacterial diversity at these sites was compared by community fingerprinting analysis using 16S rRNA gene based denaturing gradient gel electrophoresis and by 16S rRNA gene sequencing and phylogenetic analyses. Results revealed functionally conserved, diatom-driven microbial mudflat communities composed of mainly novel, uncultured species. Species composition was evaluated as 50-70% unique for each site along the BES. Clustering of the sequences commonly occurred and revealed that proteobacterial diversity was related to the salinity gradient. When considering all phyla, the diversity varied consistently with physical parameters (including anthropogenic) that are expected to influence microbial composition.ConclusionThe BES mudflats were found to comprise the typical functional groups of microorganisms associated with photosynthetic carbon flux, sulfur cycling (Gamma- and Deltaproteobacteria), and decomposition (Bacteroidetes). From a structural perspective, however, the mudflats constituted discretely distributed communities along the physical gradient of the BES, composed of largely novel species of Bacteria. This study provides first insights into patterns of bacterial community structure in tropical South East Asian coastal ecosystems that are potentially threatened by increasing variability in pH and salinity, in line with predicted future environmental change.

Microbial diversity in waters, sediments and microbial mats evaluated using fatty acid-based methods

The review summarises recent advances towards a greater comprehensive assessment of microbial diversity in aquatic environments using the fatty acid methyl esters and phospholipid fatty acids approaches. These methods are commonly used in microbial ecology because they do not require the culturing of micro-organisms, are quantitative and reproducible and provide valuable information regarding the structure of entire microbial communities. Because some fatty acids are associated with taxonomic and functional groups of micro-organisms, they allow particular groups of micro-organisms to be distinguished. The integration of fatty acid-based methods with stable isotopes, RNA and DNA analyses enhances our knowledge of the role of micro-organisms in global nutrient cycles, functional activity and phylogenetic lineages within microbial communities. Additionally, the analysis of fatty acid profiles enables the shifts in the microbial diversity in pristine and contaminated environments to be monitored. The main objective of this review is to present the use of lipid-based approaches for the characterisation of microbial communities in water columns, sediments and biomats.

The metabolic and ecological interactions of oxalate-degrading bacteria in the Mammalian gut.

Oxalate-degrading bacteria comprise a functional group of microorganisms, commonly found in the gastrointestinal tract of mammals. Oxalate is a plant secondary compound (PSC) widely produced by all major taxa of plants and as a terminal metabolite by the mammalian liver. As a toxin, oxalate can have a significant impact on the health of mammals, including humans. Mammals do not have the enzymes required to metabolize oxalate and rely on their gut microbiota for this function. Thus, significant metabolic interactions between the mammalian host and a complex gut microbiota maintain the balance of oxalate in the body. Over a dozen species of gut bacteria are now known to degrade oxalate. This review focuses on the host-microbe and microbe-microbe interactions that regulate the degradation of oxalate by the gut microbiota. We discuss the pathways of oxalate throughout the body and the mammalian gut as a series of differentiated ecosystems that facilitate oxalate degradation. We also explore the mechanisms and functions of microbial oxalate degradation along with the implications for the ecological and evolutionary interactions within the microbiota and for mammalian hosts. Throughout, we consider questions that remain, as well as recent technological advances that can be employed to answer them.

Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment

In this study, we demonstrate the possibility of obtaining a targeted metatranscriptome from a functional group of microorganisms using a stable isotope probing (SIP) approach. Methanotrophs in lake sediment were labelled using (13)CH4, and both labelled and unlabelled-RNA were isolated and sequenced by 454 pyrosequencing. The unlabelled metatranscriptome had a large diversity of bacterial, archaeal, eukaryotic and viral sequences as expected from a diverse sediment community. In contrast, the labelled-RNA metatranscriptome was dominated by methanotroph sequences, particularly from Methylococcaceae. Transcripts of the methane monooxygenase genes pmoCAB were the most abundant in this metatranscriptome, and the pathway of methane oxidation to CO2 could be traced, as well as many steps in the ribulose monophosphate pathway for carbon assimilation. A high abundance of mRNA transcripts for proteins related to motility was detected, suggesting an importance for methanotrophs in lake sediments. This combination of SIP and metatranscriptomics should be broadly applicable, and will enhance the detection and identification of mRNA from target organisms.

The variable response of soil microorganisms to trace concentrations of low molecular weight organic substrates of increasing complexity

Elevated CO2 respiration rates have been observed in soils treated with complex mixtures versus single low molecular weight (LMW) organic substrates, and it has been postulated that a more diverse range of soil microorganisms responds to increasingly complex mixtures of LMW organic substrates. To test this hypothesis, 13C-labelled substrates (glycine, an amino acid mixture and an extract of water soluble compounds from plant roots) were applied at 15 μg C g−1 soil to an arable top soil. The soils were incubated and destructively sampled after 8, 24, 48, 120 and 240 h, and the 13C content of biomarker PLFA for Gram negative bacteria, Gram positive bacteria, Actinobacteria and fungi was determined. There was no significant increase in the concentration of the biomarker PLFA, apart from Actinobacteria at the end of the incubation (120 and 240 h). However there were significant changes in total PLFA concentration due to increases in the 16:0 and 18:0 PLFA, which cannot be assigned to specific functional groups of microorganisms. 13C incorporation into the biomarker PLFA of all microbial groups was significant at every time point, but more 13C was determined in the biomarker PLFA of all microbial groups after the application of the amino acid mixture compared to glycine. Calculations of the proportion of the incorporated of 13C in the different biomarker PLFA suggested the routing of substrate 13C between the microbial groups over time. This was related to the broad functional ecology (‘r’ or ‘K’ strategy) of the different microbial groups. In conclusion, we observed that the response of all microbial groups (detected as 13C incorporation) was increased by the addition of more complex mixtures of LMW organic substrates, but that different microbial groups responded differently over time.

Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.

The Genus Lactobacillus: A Taxonomic Update.

Lactic Acid Bacteria (LAB) are a functional group of microorganisms comprising Gram-positive, catalase negative bacteria that produce lactic acid as the major metabolic end-product of carbohydrate fermentation. Among LAB, Lactobacillus is the genus including a high number of GRAS species (Generally Recognized As Safe) and many strains are among the most important bacteria in food microbiology and human nutrition, due to their contribution to fermented food production or their use as probiotics. From a taxonomic point of view, the genus Lactobacillus includes at present (October 2012), 152 validly described species, and it belongs to the family Lactobacillaceae together with genus Pediococcus, with whom it is phylogenetically intermixed. The updated phylogenetic analysis based on 16S rRNA gene sequence revealed that the family is divided into 15 groups of three or more species, 4 couples and 10 single lines of descents. In addition, other taxonomically relevant information for Lactobacillus species was collected. This study aims at updating the taxonomy of the genus Lactobacillus, presenting the phylogenetic structure of the Lactobacillaceae and discussing the clusters as possible nuclei of genera to be described in the future. It is expected that scientists and producers in the field of probiotics could benefit from information reported here about the correct identification procedures and nomenclature of beneficial strains of lactobacilli.

Mapping the niche space of soil microorganisms using taxonomy and traits

The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing.

Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.

Tools providing new insight into coastal anoxygenic purple bacterial mats: review and perspectives

Coastal photosynthetic microbial mats are highly structured microbial communities that populate a variety of shallow environments such as estuaries, sheltered sandy beaches, intertidal flats, salt marshes and hypersaline salterns. In soft sediments, most of these microbial mats are formed of vertically stratified, multicolored cohesive thin layers, of several functional groups of microorganisms, such as cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria and sulfate-reducing bacteria, distributed along vertical microgradients of oxygen, sulfide and light. These microbial communities are highly productive and significant contributors to carbon, nitrogen and sulfur cycles and to sediment stability in shallow-water habitats. Many examples of these communities have been cited in the past, but comparatively few microbial mats have been presented for which mass developments of anoxygenic purple bacteria have been observed. Yet, application of molecular approaches has provided fresh insight into the ecology, diversity and evolution of microbial mats. In situ measurements using electrochemical and optical microprobes led to detailed characterization of their physical and chemical environment, whereas reflectance measurements revealed the spatial and temporal heterogeneity of microbial mat surfaces. We hereby report the main discoveries due to introduction of these powerful techniques and we point out the potential insight to be gained from the study of anoxygenic purple bacterial mats.

Anaerobic Oxidation of Methane: Progress with an Unknown Process

Methane is the most abundant hydrocarbon in the atmosphere, and it is an important greenhouse gas, which has so far contributed an estimated 20% of postindustrial global warming. A great deal of biogeochemical research has focused on the causes and effects of the variation in global fluxes of methane throughout earth's history, but the underlying microbial processes and their key agents remain poorly understood. This is a disturbing knowledge gap because 85% of the annual global methane production and about 60% of its consumption are based on microbial processes. Only three key functional groups of microorganisms of limited diversity regulate the fluxes of methane on earth, namely the aerobic methanotrophic bacteria, the methanogenic archaea, and their close relatives, the anaerobic methanotrophic archaea (ANME). The ANME represent special lines of descent within the Euryarchaeota and appear to gain energy exclusively from the anaerobic oxidation of methane (AOM), with sulfate as the final electron acceptor according to the net reaction: CH(4) + SO(42-) ---> HCO(3-) + HS(-) + H(2)O. This review summarizes what is known and unknown about AOM on earth and its key catalysts, the ANME clades and their bacterial partners.

Changes of the functional diversity of soil microbial community during the colonization of abandoned grassland by a forest

The impact of secondary succession of grassland communities towards a Norway spruce forest on soil microbial community was studied on a belt transect established in the Pol’ana Mts., Central Europe. Data on understory vegetation, light availability, soil properties and microbial activity were collected on 147 plots distributed over regular grid. Moreover, distributions of functional groups of microorganisms were assessed using BIOLOG analysis on a subset of 27 plots. Mantel partial correlations between microbial community indicators and environmental variables showed that microbial activity generally decreased with increasing tree density and size, whereas it increased with increasing radiation at the soil surface, soil temperature, and cover and diversity of understory vegetation. Functional richness and diversity of microorganisms were positively correlated with solar radiation, but also with plant species richness and diversity. Abundance of several functional groups correlated closely with succession-related variables. Redundance analysis of microbial data provided slightly different outcomes. Forward selection yielded only two environmental variables significantly influencing the composition of the microbial community: tree influence potential and organic carbon content. Abundances of several functional microbial groups correlated with tree influence, documenting that microbial community changes are at least partially driven by the colonization of grassland by trees. Nevertheless, the relative importance of abiotic environment change and plant community succession on microbial community dynamics remains unresolved.

Investigating unsaturated fat, monensin, or bromoethanesulfonate in continuous cultures retaining ruminal protozoa. II. Interaction of treatment and presence of protozoa on prokaryotic communities

Increasing the consistency of responses to reduce emissions of ruminal methane and nitrogenous wastes into the environment using microbial inhibitors requires an accurate assessment of microbial community profiles. In addition to direct inhibition of methanogens by feed additives, protozoa are often targeted for inhibition because their close physical association with endo- and ectosymbionts stimulates methanogenesis in the rumen. In this study, we first modified a continuous culture system to maintain a diverse protozoal population (faunated subperiod) and then selectively effluxed them without using any chemical agents (defaunated subperiod). In both subperiods, unsaturated fat (potentially inhibitory to ciliate protozoa, methanogens, and gram-positive bacteria), monensin (assumed to inhibit gram-positive bacteria), and bromoethanesulfonate (BES; a potent inhibitor of methanogens) were used to suppress the respective functional groups of microorganisms. Changes in microbial populations were determined using denaturing gradient gel electrophoresis, followed by cloning and DNA sequencing of the excised bands. Neither monensin nor unsaturated fat consistently affected methanogen populations under our conditions in either the faunated or defaunated subperiods. When BES was administered, bands presumptively linked to protozoa-associated methanogens in the faunated subperiod disappeared in the defaunated subperiod. However, there was no noticeable adaptation of the sensitive methanogens to BES. The effect of dietary treatments on bacterial populations in the fermenters was harder to ascertain because of the overriding period effect caused by a different inoculum in each period. Defaunation selectively decreased the intensity of bands associated with ruminococci and clostridia but seemed to increase some Butyrivibrio and related populations. Presence of protozoa influenced both bacterial and archaeal populations, probably by selective predation, competition for substrate, or through symbiotic interactions.

Development and evaluation of a high‐performance liquid chromatography/isotope ratio mass spectrometry methodology for δ13C analyses of amino sugars in soil

Amino sugars have been used as biomarkers to assess the relative contribution of dead microbial biomass of different functional groups of microorganisms to soil carbon pools. However, little is known about the dynamics of these compounds in soil. The isotopic composition of individual amino sugars can be used as a tool to determine the turnover of these compounds. Methods to determine the delta(13)C of amino sugars using gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) have been proposed in literature. However, due to derivatization, the uncertainty on the obtained delta(13)C is too high to be used for natural abundance studies. Therefore, a new high-performance liquid chromatography/isotope ratio mass spectrometry (HPLC/IRMS) methodology, with increased accuracy and precision, has been developed. The repeatability on the obtained delta(13)C values when pure amino sugars were analyzed were not significantly concentration-dependent as long as the injected amount was higher than 1.5 nmol. The delta(13)C value of the same amino sugar spiked to a soil deviated by only 0.3 per thousand from the theoretical value.

Effect of environmental conditions on the distribution of functional groups of microorganisms in the Khoito-Gol mineral springs (East Sayan)

The structure and functional activity of the microbial communities formed under different environmental conditions of the Khoito-Gol mineral springs are investigated. The habitat of microorganisms in the Khoito-Gol springs is characterized by abundant hydrogen sulfide and intense circulation of sulfur with the participation of sulfate-reducing, thionic, colorless, and purple bacteria. The main terminal process of microbial destruction of organic matter is sulfate reduction.

Assessment of metabolic diversity within the intestinal microbiota from healthy humans using combined molecular and cultural approaches

The human gut harbours a wide range of bacterial communities that play key roles in supplying nutrients and energy to the host through anaerobic fermentation of dietary components and host secretions. This fermentative process involves different functional groups of microorganisms linked in a trophic chain. Although the diversity of the intestinal microbiota has been studied extensively using molecular techniques, the functional aspects of this biodiversity remain mostly unexplored. The aim of the present work was to enumerate the principal metabolic groups of microorganisms involved in the fermentative process in the gut of healthy humans. These functional groups of microorganisms were quantified by a cultural approach, while the taxonomic composition of the microbiota was assessed by in situ hybridization on the same faecal samples. The functional groups of microorganisms that predominated in the gut were the polysaccharide-degrading populations involved in the breakdown of the most readily available exogenous and endogenous substrates and the predominant butyrate-producing species. Most of the functional groups of microorganisms studied appeared to be present at rather similar levels in all healthy volunteers, suggesting that optimal numbers of these various bacterial groups are crucial for efficient gut fermentation, as well as for host nutrition and health. Significant interindividual differences were, however, confirmed with respect to the numbers of methanogenic archaea, filter paper-degrading and acetogenic bacteria and the products formed by lactate-utilizing bacteria.

Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processes

Identification of the functional groups of microorganisms that are predominantly in control of fluxes through, and concentrations in, microbial networks would benefit microbial ecology and environmental biotechnology: the properties of those controlling microorganisms could be studied or monitored specifically or their activity could be modulated in attempts to manipulate the behaviour of such networks. Herein we present ecological control analysis (ECA) as a versatile mathematical framework that allows for the quantification of the control of each functional group in a microbial network on its process rates and concentrations of intermediates. In contrast to current views, we show that rates of flow of matter are not always limited by a single functional group; rather flux control can be distributed over several groups. Also, control over intermediate concentrations is always shared. Because of indirect interactions, through other functional groups, the concentration of an intermediate can also be controlled by functional groups not producing or consuming it. Ecological control analysis is illustrated by a case study on the anaerobic degradation of organic matter, using experimental data obtained from the literature. During anaerobic degradation, fermenting microorganisms interact with terminal electron-accepting microorganisms (e.g. halorespirers, methanogens). The analysis indicates that flux control mainly resides with fermenting microorganisms, but can shift to the terminal electron-accepting microorganisms under less favourable redox conditions. Paradoxically, halorespiring microorganisms do not control the rate of perchloroethylene and trichloroethylene degradation even though they catalyse those processes themselves.

Detection and cultivation of indigenous microorganisms in Mesozoic claystone core samples from the Opalinus Clay Formation (Mont Terri Rock Laboratory)

Although microorganisms have been isolated from various deep-subsurface environments, the persistence of microbial activity in claystones buried to great depths and on geological time scales has been poorly studied. The presence of in-situ microbial life in the Opalinus Clay Formation (Mesozoic claystone, 170 million years old) at the Mont Terri Rock Laboratory, Canton Jura, Switzerland was investigated. Opalinus Clay is a host rock candidate for a radioactive waste repository. Particle tracer tests demonstrated the uncontaminated nature of the cored samples, showing their suitability for microbiological investigations. To determine whether microorganisms are a consistent and characteristic component of the Opalinus Clay Formation, two approaches were used: (i) the cultivation of indigenous micoorganisms focusing mainly on the cultivation of sulfate-reducing bacteria, and (ii) the direct detection of molecular biomarkers of bacteria. The goal of the first set of experiments was to assess the presence of cultivable microorganisms within the Opalinus Clay Formation. After few months of incubation, the number of cell ranged from 0.1 to 2 × 10 3 cells ml −1 media. The microorganisms were actively growing as confirmed by the observation of dividing cells, and detection of traces of sulfide. To avoid cultivation bias, quantification of molecular biomarkers (phospholipid fatty acids) was used to assess the presence of autochthonous microorganisms. These molecules are good indicators of the presence of living cells. The Opalinus Clay contained on average 64 ng of PLFA g −1 dry claystone. The detected microbial community comprises mainly Gram-negative anaerobic bacteria as indicated by the ratio of iso/anteiso phospholipids (about 2) and the detection of large amount of β-hydroxy substituted fatty acids. The PLFA composition reveals the presence of specific functional groups of microorganisms in particular sulfate-reducing bacteria ( Desulfovibrio, Desulfobulbus, and Desulfobacter). This study demonstrates that microorganisms are a characteristic component of the unperturbed Opalinus Clay Formation.

Microbial co-operation in the rhizosphere

Soil microbial populations are immersed in a framework of interactions known to affect plant fitness and soil quality. They are involved in fundamental activities that ensure the stability and productivity of both agricultural systems and natural ecosystems. Strategic and applied research has demonstrated that certain co-operative microbial activities can be exploited, as a low-input biotechnology, to help sustainable, environmentally-friendly, agro-technological practices. Much research is addressed at improving understanding of the diversity, dynamics, and significance of rhizosphere microbial populations and their co-operative activities. An analysis of the co-operative microbial activities known to affect plant development is the general aim of this review. In particular, this article summarizes and discusses significant aspects of this general topic, including (i) the analysis of the key activities carried out by the diverse trophic and functional groups of micro-organisms involved in co-operative rhizosphere interactions; (ii) a critical discussion of the direct microbe-microbe interactions which results in processes benefiting sustainable agro-ecosystem development; and (iii) beneficial microbial interactions involving arbuscular mycorrhiza, the omnipresent fungus-plant beneficial symbiosis. The trends of this thematic area will be outlined, from molecular biology and ecophysiological issues to the biotechnological developments for integrated management, to indicate where research is needed in the future.