Soil microbial community structure across a thermal gradient following a geothermal heating event

Association between host nitrogen absorption and root-associated microbial community in field-grown wheat

Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.

Microbial consortia and up-to-date technologies in global soy sauce production: A review

Soy sauce is an Oriental fermented condiment, and key ingredient in many Asian cuisines. As consumers around the world are becoming more adventurous with their eating choices and preferences, the demand for and popularity of Asian cuisines are increasing globally. The underlying basis of soy sauce fermentation is intricate microbial interactions which play a vital role in defining the quality, flavour, and smell of the resulting soy sauce. Traditional soy sauce fermentation consists of a two-step process: koji and moromi fermentation. Despite the presence of beneficial microorganisms in soy sauce, various harmful microorganisms can also be found during the koji or moromi step, thus resulting in soy sauce contamination. Therefore, studying the biodiversity and interactions of microorganisms is critical in ensuring soy sauce quality. The present review thus discusses in depth the various bacterial and fungal species that are either beneficial or harmful to soy sauce fermentation. The present review also discusses the advances in soy sauce fermentation such as the enhancement of gamma-aminobutyric acid (GABA) in soy sauce by microorganisms, the enhancement of soy sauce flavour by mixed starter culture, and by genome shuffling starter culture.

Distribution and diversity of anaerobic thermophiles and putative anaerobic nickel-dependent carbon monoxide-oxidizing thermophiles in mesothermal soils and sediments

Even though thermophiles are best known from geothermal and other heated systems, numerous studies have demonstrated that they occur ubiquitously in mesothermal and permanently cold soils and sediments. Cultivation based studies of the latter have revealed that the thermophiles within them are mostly spore-forming members of the Firmicutes. Since the geographic distribution of spores is presumably unconstrained by transport through the atmosphere, similar communities (composition and diversity) of thermophiles might be expected to emerge in mesothermal habitats after they are heated. Alternatively, thermophiles might experience environmental selection before or after heating leading to divergent communities. After demonstrating the ubiquity of anaerobic thermophiles and CO uptake in a variety of mesothermal habitats and two hot springs, we used high throughput sequencing of 16S rRNA genes to assess the composition and diversity of populations that emerged after incubation at 60°C with or without headspace CO concentrations of 25%. Anaerobic Firmicutes dominated relative abundances at most sites but anaerobic thermophilic members of the Acidobacteria and Proteobacteria were also common. Nonetheless, compositions at the amplicon sequence variant (ASV) level varied among the sites with no convergence resulting from heating or CO addition as indicated by beta diversity analyses. The distinctions among thermophilic communities paralleled patterns observed for unheated "time zero" mesothermal soils and sediments. Occupancy analyses showed that the number of ASVs occupying each of n sites decreased unimodally with increasing n; no ASV occupied all 14 sites and only one each occupied 11 and 12 sites, while 69.3% of 1873 ASVs occupied just one site. Nonetheless, considerations of distances among the sites occupied by individual ASVs along with details of their distributions indicated that taxa were not dispersal limited but rather were constrained by environmental selection. This conclusion was supported by βMNTD and βNTI analyses, which showed dispersal limitation was only a minor contributor to taxon distributions.

Increased water inputs fuel microbial mercury methylation in upland soils

Mercury (Hg) can be converted to neurotoxic methylmercury (MeHg) by certain microbes typically in anaerobic environments, threatening human health due to its bioaccumulation in food webs. However, it is unclear whether and how Hg can be methylated in legacy aerobic uplands with increasing water. Here, we conducted a series of incubation experiments to investigate the effects of increased water content on MeHg production in two typical upland soils (i.e., long-term and short-term use). Results showed that marked MeHg production occurred in water-saturated upland soils, which was strongly correlated with the proportions of significantly stimulated Hg methylating taxon (i.e., Geobacter). Elevated temperature further enhanced MeHg production by blooming proportions of typical Hg methylators (i.e., Clostridium, Acetonema, and Geobacter). Water saturation could also enhance microbial Hg methylation by facilitating microbial syntrophy between non-Hg methylators and Hg methylators. Taken together, the present work suggests that uplands could turn into a potential MeHg reservoir in response to water inputs resulting from rainfall or anthropogenic irrigation.

Bacterial diversity in 110 thermal hot springs of Indian Himalayan Region (IHR)

Thermal hot springs are present throughout the world and constitute a unique habitat for microbial diversity. The current investigation is conducted to study the bacterial diversity of thermophilic microorganisms in thermal hot springs of the Indian Himalayan Region (IHR). As of today, 110 geothermal hot springs have been explored for microbial diversity. In this study, we observed that the growth of thermophilic bacteria isolated from thermal hot springs of IHR ranges between 40 and 100 °C, and pH of 3.5-8 have been reported in the literature. The major bacterial species reported from the thermal hot springs of IHR are Bacillus spp., Geobacillus spp., Paenibacillus spp., Pseudomonas spp., Anoxybacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Thermus aquaticus, Aquimonas, Flavobacterium, etc. Furthermore, bacterial isolates from thermal hot springs of IHR have been reported to produce various enzymes and metabolites such as amylase, β-galactosidase, cellulase, nitrate reductase, acetoin, caffeine degradation enzymes, lipase, urease, and laccase. Metagenomic study and the entire genomic shotgun project have established the impact of physicochemical parameters (temperature and pH) on developing the microbiome. We have discussed the discoveries of microbiological data on the hot springs of IHR until the end of year 2021. As a whole, the microbiome adapts themselves as successful inhabitants to extreme environmental conditions and also serves as a diverse resource for potential applications in health, food, and environment.

Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica

Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.

GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring

GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria. We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 10⁵ 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria, representing a candidate order (Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O₂, suggesting a microaerophilic lifestyle.

Soil microbial sensitivity to temperature remains unchanged despite community compositional shifts along geothermal gradients

Climate warming may be exacerbated if rising temperatures stimulate losses of soil carbon to the atmosphere. The direction and magnitude of this carbon-climate feedback are uncertain, largely due to lack of knowledge of the thermal adaptation of the physiology and composition of soil microbial communities. Here, we applied the macromolecular rate theory (MMRT) to describe the temperature response of the microbial decomposition of soil organic matter (SOM) in a natural long-term warming experiment in a geothermally active area in New Zealand. Our objective was to test whether microbial communities adapt to long-term warming with a shift in their composition and their temperature response that are consistent with evolutionary theory of trade-offs between enzyme structure and function. We characterized the microbial community composition (using metabarcoding) and the temperature response of microbial decomposition of SOM (using MMRT) of soils sampled along transects of increasing distance from a geothermally active zone comprising two biomes (a shrubland and a grassland) and sampled at two depths (0-50 and 50-100 mm), such that ambient soil temperature and soil carbon concentration varied widely and independently. We found that the different environments were hosting microbial communities with distinct compositions, with thermophile and thermotolerant genera increasing in relative abundance with increasing ambient temperature. However, the ambient temperature had no detectable influence on the MMRT parameters or the relative temperature sensitivity of decomposition (Q₁₀ ). MMRT parameters were, however, strongly correlated with soil carbon concentration and carbon:nitrogen ratio. Our findings suggest that, while long-term warming selects for warm-adapted taxa, substrate quality and quantity exert a stronger influence than temperature in selecting for distinct thermal traits. The results have major implications for our understanding of the role of soil microbial processes in the long-term effects of climate warming on soil carbon dynamics and will help increase confidence in carbon-climate feedback projections.

Prokaryotic and eukaryotic diversity in hydrothermal continental systems

The term extremophile was suggested more than 30 years ago and represents microorganisms that are capable of developing and living under extreme conditions, these conditions being particularly hostile to other types of microorganisms and to humankind. In terrestrial hydrothermal sites, like hot springs, "mud pools", solfataras, and geysers, the dominant extreme conditions are high temperature, low or high pH, and high levels of salinity. The diversity of microorganisms inhabiting these sites is determined by the conditions of the environment. Organisms belonging to the domains Archaea and Bacteria are more represented than the one belonging to Eukarya. Eukarya members tend to be less present because of their lower tolerance to higher temperatures, however, they perform important ecosystem processes when present. Both prokaryotes and eukaryotes have morphological and physical adaptations that allow them to colonize extreme environments. Microbial mats are complex associations of microorganisms that help the colonization of more extreme systems. In this review, a characterization of prokaryotic and eukaryotic organisms that populate terrestrial hydrothermal systems are made.

Composition and predicted functions of the bacterial community in spouting pool sediments from the El Tatio Geyser field in Chile

The El Tatio Geyser Field (ETGF), located in Northern Chile, is the main geyser field in the southern hemisphere. Despite this, details of its microbial ecology are still unknown. Here, we briefly report on  the composition and predicted functions of the bacterial community in spouting pool sediments from the ETGF as revealed by high-throughput sequencing of 16S rRNA genes. Results of this analysis showed that while there were differences in richness and diversity between samples, bacterial communities were primarily dominated by the phyla Proteobacteria, followed Firmicutes, Bacteroidetes, Acidobacteria, and Chloroflexi. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by sulfur (respiration of sulfur compounds and sulfate) and nitrogen (nitrate reduction, respiration of nitrogen and nitrate) cycling. Taken together, our results suggest a high diversity in taxonomy and predictive functions of bacterial communities in sediments from spouting pools. This study provides fundamentally important  information on the structure and function  predictive functions of microbiota  communities in spouting pools. Moreover, since the ETGF is intensively visited and impacted by tens of thousands of tourists every year, our results can be used to help guide the design of sustainable conservation strategies.

Diversity of Growth Responses of Soil Saprobic Fungi to Recurring Heat Events

As a consequence of ongoing climate change, the frequency of extreme heat events is expected to increase. Recurring heat pulses may disrupt functions supported by soil microorganisms, thus affecting the entire ecosystem. However, most perturbation experiments only test effects of single heat events, and therefore it remains largely unknown how soil microorganisms react to repeated pulse events. Here we present data from a lab experiment exposing 32 filamentous fungi, originally isolated from the same soil, to sequential heat perturbations. Soil saprobic fungi isolates were exposed to one or two heat pulses: mild (35°C/2 h), strong (45°C/1 h), or both in sequence (35°C/2 h+45°C/1 h), and we assessed growth rate. Out of the 32 isolates 13 isolates showed an antagonistic response, 3 isolates a synergistic response and 16 isolates responded in an additive manner. Thus the 32 filamentous fungal isolates used here showed the full range of possible responses to an identical heat perturbation sequence. This diversity of responses could have consequences for soil-borne ecosystem services, highlighting the potential importance of fungal biodiversity in maintaining such services, particularly in the context of climate change.

A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms

Network analysis was used to show changes in network attributes by analyzing the relations among the main soil microbial groups in a potted tomato soil inoculated with arbuscular mycorrhizal fungus, treated with low doses of Mentha spicata essential oil, or both, and then exposed to tenfold higher oil addition (stress pulse). Pretreatments were chosen since they can induce changes in the composition of the microbial community. Cellular phospholipid fatty acids (PLFAs) and the activity of six soil enzymes, mainly involved in the N-cycle were measured. Networks were constructed based on correlated changes in PLFA abundances. The values of all parameters were significantly different from those of random networks indicating modular architecture. Networks ranked from the lowest to highest modularity: control, non-pretreated and stressed, inoculated and stressed, oil treated and stressed, inoculated and treated with oil and stressed. The high values of network density and 1st/2nd eigenvalue ratio are related to arylamidase activity while N-acetyl-glucosaminidase, acid phosphomoesterase, and asparaginase activities related to high values of the clustering coefficient index. We concluded that modularity may be an efficient indicator of changes in the network of interactions among the members of the soil microbial community and the modular structure of the network may be related to the activity of specific enzymes. Communities that were stressed without a pretreatment were relatively resistant but prone to sudden transition towards instability, while oil or inoculation pretreatments gave networks which could be considered adaptable and susceptible to gradual change.

Microbiomes in Soils Exposed to Naturally High Concentrations of CO2 (Bossoleto Mofette Tuscany, Italy)

Direct and indirect effects of extremely high geogenic CO₂ levels, commonly occurring in volcanic and hydrothermal environments, on biogeochemical processes in soil are poorly understood. This study investigated a sinkhole in Italy where long-term emissions of thermometamorphic-derived CO₂ are associated with accumulation of carbon in the topsoil and removal of inorganic carbon in low pH environments at the bottom of the sinkhole. The comparison between interstitial soil gasses and those collected in an adjacent bubbling pool and the analysis of the carbon isotopic composition of CO₂ and CH₄ clearly indicated the occurrence of CH₄ oxidation and negligible methanogenesis in soils at the bottom of the sinkhole. Extremely high CO₂ concentrations resulted in higher microbial abundance (up to 4 × 10⁹ cell g^-1 DW) and a lower microbial diversity by favoring bacteria already reported to be involved in acetogenesis in mofette soils (i.e., Firmicutes, Chloroflexi, and Acidobacteria). Laboratory incubations to test the acetogenic and methanogenic potential clearly showed that all the mofette soil supplied with hydrogen gas displayed a remarkable CO₂ fixation potential, primarily due to the activity of acetogenic microorganisms. By contrast, negligible production of acetate occurred in control tests incubated with the same soils, under identical conditions, without the addition of hydrogen. In this study, we report how changes in diversity and functions of the soil microbial community - induced by high CO₂ concentration - create peculiar biogeochemical profile. CO₂ emission affects carbon cycling through: (i) inhibition of the decomposition of the organic carbon and (ii) promotion of CO₂-fixation via the acetyl-CoA pathway. Sites naturally exposed to extremely high CO₂ levels could potentially represent an untapped source of microorganisms with unique capabilities to catalytically convert CO₂ into valuable organic chemicals and fuels.

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites

This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils.

Climate change and geothermal ecosystems: natural laboratories, sentinel systems, and future refugia

Understanding and predicting how global warming affects the structure and functioning of natural ecosystems is a key challenge of the 21st century. Isolated laboratory and field experiments testing global change hypotheses have been criticized for being too small-scale and overly simplistic, whereas surveys are inferential and often confound temperature with other drivers. Research that utilizes natural thermal gradients offers a more promising approach and geothermal ecosystems in particular, which span a range of temperatures within a single biogeographic area, allow us to take the laboratory into nature rather than vice versa. By isolating temperature from other drivers, its ecological effects can be quantified without any loss of realism, and transient and equilibrial responses can be measured in the same system across scales that are not feasible using other empirical methods. Embedding manipulative experiments within geothermal gradients is an especially powerful approach, informing us to what extent small-scale experiments can predict the future behaviour of real ecosystems. Geothermal areas also act as sentinel systems by tracking responses of ecological networks to warming and helping to maintain ecosystem functioning in a changing landscape by providing sources of organisms that are preadapted to different climatic conditions. Here, we highlight the emerging use of geothermal systems in climate change research, identify novel research avenues, and assess their roles for catalysing our understanding of ecological and evolutionary responses to global warming.

Morphological and phylogenetic diversity of thermophilic cyanobacteria in Algerian hot springs

Geothermal springs in Algeria have been known since the Roman Empire. They mainly locate in Eastern Algeria and are inhabited by thermophilic organisms, which include cyanobacteria forming mats and concretions. In this work, we have investigated the cyanobacterial diversity of these springs. Cyanobacteria were collected from water, concretions and mats in nine hot springs with water temperatures ranging from 39 to 93 °C. Samples were collected for isolation in culture, microscopic morphological examination, and molecular diversity analysis based on 16S rRNA gene sequences. Nineteen different cyanobacterial morphotypes were identified, the most abundant of which were three species of Leptolyngbya, accompanied by members of the genera Gloeocapsa, Gloeocapsopsis, Stigonema, Fischerella, Synechocystis, Microcoleus, Cyanobacterium, Chroococcus and Geitlerinema. Molecular diversity analyses were in good general agreement with classical identification and allowed the detection of additional species in three springs with temperatures higher than 50 °C. They corresponded to a Synechococcus clade and to relatives of the intracellularly calcifying Candidatus Gloeomargarita lithophora. The hottest springs were dominated by members of Leptolyngbya, Synechococcus-like cyanobacteria and Gloeomargarita, whereas Oscillatoriales other than Leptolyngbya, Chroococcales and Stigonematales dominated lower temperature springs. The isolation of some of these strains sets the ground for future studies on the biology of thermophilic cyanobacteria.

Steam-treatment-based soil remediation promotes heat-tolerant, potentially pathogenic microbiota

We investigated microbiota in surface and subsurface soil from a site, above steam-treated deep sub-soil originally contaminated with chlorinated solvents. During the steam treatment, the surface soil reached temperatures c. 30 degrees C higher than the temperature in untreated soil; whereas the subsurface soil, at a depth of about 40 cm, reached a temperature c. 45 degrees C higher than untreated soil. The soil was examined prior to, during, and 6, 12, 14, 20 and 31 months after treatment. Numbers of bacteria cultivable at 42 degrees C increased significantly in subsurface soil. Similarly, substrate utilization in ECOLOG plates, incubated at 42 degrees C, increased from less than 10% of available carbon sources in the untreated soil to more than 60% of the available carbon sources in the steam-treated soil. Aspergillus fumigatus was quantified as an example ofheat-tolerant fungi normally found in compost. These organisms are rarely detected in Danish soils but high numbers (c. 10(5) hyphal forming units g(-1)) occurred in the treated soil up to 31 months after the steam-treatment. We conclude that steam-treatment leads to changes of the microbial communities. Some changes are temporary while others can last for years after termination of the steam-treatment; reflecting different strategies that soil microorganisms follow.

Microbial community diversities and taxa abundances in soils along a seven-year gradient of potato monoculture using high throughput pyrosequencing approach

BACKGROUND

Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach.

METHODOLOGY/PRINCIPAL FINDINGS

Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H(Shannon)) and richness (S(Chao1)) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time.

CONCLUSIONS

Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait. Correlations between abundance of Fusarium with several other bacterial taxa suggested their similar behaviors in responses to potato monoculture and/or soil variables, providing insights into the ecological behaviors of these taxa in the environment.

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

Paenibacillus thermoaerophilus sp. nov., a moderately thermophilic bacterium isolated from compost

A rod-shaped, endospore-forming, Gram-reaction-positive bacterium, designated strain TC22-2bT, was isolated from compost in Tochigi, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to a cluster comprising species of the genus Paenibacillus and was most closely related to the type strain of Paenibacillus elgii (93.4 % similarity). The major cellular fatty acids were C16:0 (25.5 %), iso-C16:0 (23.6 %) and anteiso-C15:0 (21.5 %). The predominant menaquinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The diamino acid found in the cell wall peptidoglycan was meso-diaminopimelic acid, and the DNA G+C content was 59.1 mol%. The results of physiological and biochemical tests enabled the phenotypic differentiation of strain TC22-2bT from the most closely related species with validly published names. Phylogenetic and phenotypic evidence reveals that strain TC22-2bT represents a novel species of the genus Paenibacillus , for which the name Paenibacillus thermoaerophilus sp. nov. is proposed. The type strain of the novel species is TC22-2bT ( = DSM 26310T  = JCM 18657T).

Short-term effects of temperature on the abundance and diversity of magnetotactic cocci

Temperature is one of the most important climate factors that can regulate the activity and growth of organisms. However, it is so far unclear how temperature influences the abundance and community composition of magnetotactic bacteria (MTB) that mineralize intracellular magnetite and/or greigite magnetosomes and play significant roles in the global iron cycling and sediment magnetization. To address this specific problem, in this study we have assessed the impact of temperature on freshwater magnetotactic cocci through laboratory microcosm simulations. Microcosms containing MTB were exposed to four constant temperatures ranging from 9°C to 37°C. After 10 days and 28 days of incubation, no significant differences in abundance were detected in microcosms at 9°C, 15°C, and 26°C (Student's t-test, P > 0.05); however, microcosms exposed to 37°C exhibited a significant decrease of magnetotactic cocci abundance (P < 0.05). Dendrogram analysis of community-amplified ribosomal DNA restriction analysis (community ARDRA) banding patterns distinguished the 37°C samples from samples at lower temperatures regardless of incubation periods. Furthermore, clone library analysis revealed that most of the operational taxonomic units (OTUs) detected in samples from 9°C to 26°C were absent from the 37°C microcosms, whereas six OTUs were exclusively detected in the 37°C samples. Community compositions from four incubation temperatures were further compared using statistical phylogenetic methods (UniFrac and LIBSHUFF), which revealed that the 37°C samples harbored phylogenetically distinct MTB communities compared to those found in 9°C, 15°C, and 26°C samples. Taken together, our results indicate that elevated temperature can influence the abundance and diversity of dominant members of magnetotactic cocci. This linkage further infers that the abundance and diversity of MTB (e.g., based on the fossil magnetosomes) may be useful in reconstruction of paleotemperature.

The effect of triclosan on microbial community structure in three soils

The application of sewage sludge to land can expose soils to a range of associated chemical toxicants. In this paper we explore the effects of the broad spectrum anti-microbial compound triclosan on the phenotypic composition of the microbial communities of three soils of contrasting texture (loamy sand, sandy loam and clay) using phospholipid fatty-acid (PLFA) analysis. Each soil type was dosed and subsequently re-dosed 6 weeks later with triclosan at five nominal concentrations in microcosms (10, 100, 500, 1000 mg kg(-1) and a zero-dose control). PLFA profiles were analysed using multivariate statistics focussing on changes in the soil phenotypic community structure. Additionally, ratios of fungal:bacterial PLFA indicators and cyclo:mono-unsaturated PLFAs (a common stress indicator) were calculated. It was hypothesised that triclosan addition would alter the community structure in each soil with a particular effect on the fungal:bacterial ratio, since bacteria are likely to be more susceptible to triclosan than fungi. It was also hypothesised that the PLFA response to re-dosing would be suppressed due to acclimation. Although the microbial community structure changed over the course of the experiment, the response was complex. Soil type and time emerged as the most important explanatory factors. Principal component analysis was used to detect phenotypic responses to different doses of triclosan in each soil. As expected, there was a significant increase in the fungal:bacterial ratio with triclosan dose especially in treatments with the highest nominal concentrations. Furthermore, the PLFA response to re-dosing was negligible in all soils confirming the acclimation hypothesis.

Diversity of prokaryotes associated with soils around coal-fire gas vents in MaNasi county of Xinjiang, China

Bacterial and archaeal diversity in surface soils of three coal-fire vents was investigated by T-RFLP analysis and clone libraries of 16S rRNA genes. Soil analysis showed that underground coal fires significantly influenced soil pH, moisture and NO(3) (-) content but had little effect on other elements, organic matter and available nutrients. Hierarchical cluster analysis showed that bacterial community patterns in the soils were very similar, but abundance varied with geographic distance. A clone library from one soil showed that the bacterial community was mainly composed of Firmicutes, Proteobacteria, Acidobacteria, Bacteroidetes, Planctomycetes, Actinobacteria, and unidentified groups. Of these, Firmicutes was the most abundant, accounting for 71.4 % of the clones, and was mainly represented by the genera Bacillus and Paenibacillus. Archaeal phylotypes were closely related to uncultivated species of the phyla Crenarchaeota (97.9 % of clones) and Thaumarchaeota (2.1 %). About 28 % of archaeal phylotypes were associated with ammonia oxidization, especially phylotypes that were highly related to a novel, ammonia-oxidizing isolate from the phylum Thaumarchaeota. These results suggested that microbial communities in the soils were diverse and might contain a large number of novel cultivable species with the potential to assimilate materials by heterotrophic metabolism at high temperature.

The effect of resource islands on abundance and diversity of bacteria in arid soils

Bacteria and nutrients were determined in upper soil samples collected underneath and between canopies of the dominant perennial in each of three sites along a steep precipitation gradient ranging from the Negev desert in the south of Israel to a Mediterranean forest in the north. Bacterial abundance, monitored by phospholipid fatty acid analysis, was significantly higher under the shrub canopy (compared to barren soils) in the arid and semi-arid sites but not in the Mediterranean soils. Bacterial community composition, determined using terminal restriction fragment length polymorphism and clone libraries, differed according to the sample's origin. Closer examination revealed that in the arid and semi-arid sites, α-Proteobacteria are more abundant under the shrub canopy, while barren soils are characterized by a higher abundance of Actinobacteria. The bacterial communities in the Mediterranean soils were similar in both patch types. These results correspond to the hypothesis of "resource islands", suggesting that shrub canopies provide a resource haven in low-resource landscapes. Yet, a survey of the physicochemical parameters of inter- and under-shrub soils could not attribute the changes in bacterial diversity to soil moisture, organic matter, or essential macronutrients. We suggest that in the nutrient-poor soils of the arid and semi-arid sites, bacteria occupying the soil under the shrub canopy may have longer growth periods under favorable conditions, resulting in their increased biomass and altered community composition.

Biophysical model of prokaryotic diversity in geothermal hot springs

Recent studies of photosynthetic bacteria living in geothermal hot spring environments have revealed surprisingly complex ecosystems with an unexpected level of genetic diversity. One case of particular interest involves the distribution along hot spring thermal gradients of genetically distinct bacterial strains that differ in their preferred temperatures for reproduction and photosynthesis. In such systems, a single variable, temperature, defines the relevant environmental variation. In spite of this, each region along the thermal gradient exhibits multiple strains of photosynthetic bacteria adapted to several distinct thermal optima, rather than a single thermal strain adapted to the local environmental temperature. Here we analyze microbiology data from several ecological studies to show that the thermal distribution data exhibit several universal features independent of location and specific bacterial strain. These include the distribution of optimal temperatures of different thermal strains and the functional dependence of the net population density on temperature. We present a simple population dynamics model of these systems that is highly constrained by biophysical data and by physical features of the environment. This model can explain in detail the observed thermal population distributions, as well as certain features of population dynamics observed in laboratory studies of the same organisms.

Role of the terrestrial subsurface in shaping geothermal spring microbial communities

In this study, we explored the possibility that dispersal from terrestrial subsurface sources 'seeds' the development of geothermal spring microbial assemblages. We combined microscopy and culture-independent molecular approaches to survey the bacterial diversity of spring source waters in Yellowstone National Park, Lassen Volcanic National Park, and Russia's Kamchatka peninsula. Microscopic analysis uncovered clear evidence of microbial cells from spring sources in all three regions. Analysis of source water phylogenetic diversity identified members of all bacteria groups found previously in downstream sediments, as well as many other phylogenetic groups. Closely related or identical 16S sequences were determined from the source waters of geographically distant, chemically distinct springs, and we found no association between spring water chemistry and microbial diversity. In the source waters of two different Yellowstone springs, we also discovered a phylogenetic group of uncultured Firmicutes never before reported in geothermal habitats that were closely related to uncultured bacteria found in the hyper-arid Atacama Desert. Altogether, our results suggest geothermal features can be connected via the subsurface over long distances and that subsurface sources provide a potentially diverse source of microorganisms for downstream surface mat communities.

Experimentally simulated global warming and nitrogen enrichment effects on microbial litter decomposers in a marsh

Atmospheric warming and increased nitrogen deposition can lead to changes of microbial communities with possible consequences for biogeochemical processes. We used an enclosure facility in a freshwater marsh to assess the effects on microbes associated with decomposing plant litter under conditions of simulated climate warming and pulsed nitrogen supply. Standard batches of litter were placed in coarse-mesh and fine-mesh bags and submerged in a series of heated, nitrogen-enriched, and control enclosures. They were retrieved later and analyzed for a range of microbial parameters. Fingerprinting profiles obtained by denaturing gradient gel electrophoresis (DGGE) indicated that simulated global warming induced a shift in bacterial community structure. In addition, warming reduced fungal biomass, whereas bacterial biomass was unaffected. The mesh size of the litter bags and sampling date also had an influence on bacterial community structure, with the apparent number of dominant genotypes increasing from spring to summer. Microbial respiration was unaffected by any treatment, and nitrogen enrichment had no clear effect on any of the microbial parameters considered. Overall, these results suggest that microbes associated with decomposing plant litter in nutrient-rich freshwater marshes are resistant to extra nitrogen supplies but are likely to respond to temperature increases projected for this century.

Good to the bone: microbial community thrives within bone cavities of a bison carcass at Yellowstone National Park

The discovery of unanticipated microbial diversity in remote, often hostile environments has led to a greater appreciation of the complexity and richness of the natural world. Yellowstone National Park (YNP) has long been a focus of work on taxa that inhabit extreme environments. Here we report the finding of microbial flora that inhabit an unexpected niche: the cavities of bone remnants from a bison carcass in Norris Geyser Basin in YNP. Although bleached white on the surface, the bone cavities are bright green due to the presence of Stichococcus-like trebouxiophyte green algae. The cavities also harbour different fungi and bacteria. Stichococcus species are common lichen photobionts and the Thelebolales fungi present in the bone cavities have previously been found in association with animal remains. Scanning electron microscope analysis suggests the fungi and algae do not form lichen-like associations in the bone. Rather these taxa and the bacteria appear to be opportunists that have colonized an isolated oasis that provides nutrients and protection from desiccation and UV radiation.

Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea

Recent DNA-based phylogenetic studies have reported high eukaryotal diversities in a wide range of settings including samples obtained from anoxic environments. However, parallel RNA-based surveys are required in order to verify whether the species detected are in fact metabolically active in such extreme environments. The Black Sea is the World's largest anoxic basin but remains undersampled with respect to molecular eukaryotic diversity studies. Here, we report the distribution of active eukaryotes (18S rRNA-based survey) along a vertical nutrient and redox gradient in the water column and surface sediments of the Black Sea. A wide variety of eukaryotes were active in suboxic deep waters. Notably, certain species were active but escaped detection during a parallel 18S rDNA survey. The 18S rDNA survey from surface sediments yielded taxa of pelagic origin but none of these were identified from the water column at the time of sampling. Our data also indicate that gene transcripts do not always provide unequivocal proof that active microorganisms are indigenous to a specific position in an environmental gradient, because certain zoo- and phytoplankton species were still viable with detectable 18S rRNA in up to 300-year-old sulfidic sediments that underlie approximately 830 m of sulfidic waters.

Microbial biodiversity of thermophilic communities in hot mineral soils of Tramway Ridge, Mount Erebus, Antarctica

Tramway Ridge, located near the summit of Mount Erebus in Antarctica, is probably the most remote geothermal soil habitat on Earth. Steam fumaroles maintain moist, hot soil environments creating extreme local physicochemical differentials. In this study a culture-independent approach combining automated rRNA intergenic spacer analysis (ARISA) and a 16S rRNA gene library was used to characterize soil microbial (Bacterial and Archaeal) diversity along intense physicochemical gradients. Statistical analysis of ARISA data showed a clear delineation between bacterial community structure at sites close to fumaroles and all other sites. Temperature and pH were identified as the primary drivers of this demarcation. A clone library constructed from a high-temperature site led to the identification of 18 novel bacterial operational taxonomic units (OTUs). All 16S rRNA gene sequences were deep branching and distantly (85-93%) related to other environmental clones. Five of the signatures branched with an unknown group between candidate division OP10 and Chloroflexi. Within this clade, sequence similarity was low, suggesting it contains several yet-to-be described bacterial groups. Five archaeal OTUs were obtained and exhibited high levels of sequence similarity (95-97%) with Crenarchaeota sourced from deep-subsurface environments on two distant continents. The novel bacterial assemblage coupled with the unique archaeal affinities reinvigorates the hypotheses that Tramway Ridge organisms are relics of archaic microbial lineages specifically adapted to survive in this harsh environment and that this site may provide a portal to the deep-subsurface biosphere.

Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin

The frontiers of eukaryote life in nature are still unidentified. In this study, we analysed protistan communities in the hypersaline (up to 365 g l(-1) NaCl) anoxic L'Atalante deep-sea basin located in the eastern Mediterranean Sea. Targeting 18S ribosomal RNA retrieved from the basin's lower halocline (3501 m depth) we detected 279 protistan sequences that grouped into 42 unique phylotypes (99% sequence similarity). Statistical analyses revealed that these phylotypes account only for a proportion of the protists inhabiting this harsh environment with as much as 50% missed by this survey. Most phylotypes were affiliated with ciliates (45%), dinoflagellates (21%), choanoflagelates (10%) and uncultured marine alveolates (6%). Sequences from other taxonomic groups like stramenopiles, Polycystinea, Acantharea and Euglenozoa, all of which are typically found in non-hypersaline deep-sea systems, are either missing or very rare in our cDNA clone library. Although many DHAB sequences fell within previously identified environmental clades, a large number branched relatively deeply. Phylotype richness, community membership and community structure differ significantly from a deep seawater reference community (3499 m depth). Also, the protistan community in the L'Atalante basin is distinctively different from any previously described hypersaline community. In conclusion, we hypothesize that extreme environments may exert a high selection pressure possibly resulting in the evolution of an exceptional and distinctive assemblage of protists. The deep hypersaline anoxic basins in the Mediterranean Sea provide an ideal platform to test for this hypothesis and are promising targets for the discovery of undescribed protists with unknown physiological capabilities.

Response of soil bacterial community structure to successive perturbations of different types and intensities

In soil, genetic structure modifications of indigenous bacterial community consecutively to a severe stress (mercury contamination) were delayed when the community was pre-exposed to various minor perturbations (heat, copper and atrazine). Such minor perturbations induced transitory community structure modifications leading to an increase of community stability towards a severe mercury stress. These results illustrated well the short-term pre-adaptation process for bacterial community hypothesizing that community submitted to perturbations become more resistant to withstand another stress.

Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development

The origins of the biological complexity and the factors that regulate the development of community composition, diversity and richness in soil remain largely unknown. To gain a better understanding of how bacterial communities change during soil ecosystem development, their composition and diversity in soils that developed over c. 77 000 years of intermittent aeolian deposition were studied. 16S rRNA gene clone libraries and fatty acid methyl ester (FAME) analyses were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. When analysed using a multivariate Bray-Curtis ordination technique, the distribution of ribotypes showed an orderly pattern of bacterial community development that was clearly associated with soil and ecosystem development. Similarly, changes in the composition of the FAMEs across the chronosequence were associated with biomarkers for fungi, actinomycetes and Gram-positive bacteria. The development of the soil ecosystem promoted the development of distinctive microbial communities that were reminiscent of successional processes often evoked to describe change during the development of plant communities in terrestrial ecosystems.

Comparative analysis of intestinal microbial community diversity between healthy and orally infected ducklings with Salmonella enteritidis by ERIC-PCR

AIM: To analyze the difference of intestinal microbial community diversity between healthy and (S. enteritidis) orally infected ducklings.

METHODS: Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR was applied to analyze the intestinal microbial community diversity and dynamic change including duodenum, jejunum, ileum, cecum and rectum from healthy ducklings and 7-day-old ducklings after oral infection with S. enteritidis at different time points.

RESULTS: The intestinal microbial community of the control healthy ducklings was steady and the ERIC-PCR band numbers of the control healthy ducklings were the least with rectum and were the most with caecum. ERIC-PCR bands of orally inoculated ducklings did not obviously change until 24 h after inoculation (p.i.). The numbers of the ERIC-PCR bands gradually decreased from 24 h to 72 h p.i., and then, with the development of disease, the band numbers gradually increased until 6 d p.i. The prominent bacteria changed because of S. enteritidis infection and the DNAstar of staple of ERIC-PCR showed that aerobe and facultative aerobe (Escherichia coli, Shigella, Salmonella) became preponderant bacilli in the intestine of orally infected ducklings with SE.

CONCLUSION: This study has provided significant data to clarify the intestinal microbial community diversity and dynamic change of healthy and S. enteritidis orally infected ducklings, and valuable insight into the pathogenesis of S. enteritidis infection in both human and animals.

Autecology of an arsenite chemolithotroph: sulfide constraints on function and distribution in a geothermal spring

Previous studies in an acid-sulfate-chloride spring in Yellowstone National Park found that microbial arsenite [As(III)] oxidation is absent in regions of the spring outflow channel where H(2)S exceeds approximately 5 microM and served as a backdrop for continued efforts in the present study. Ex situ assays with microbial mat samples demonstrated immediate As(III) oxidation activity when H(2)S was absent or at low concentrations, suggesting the presence of As(III) oxidase enzymes that could be reactivated if H(2)S is removed. Cultivation experiments initiated with mat samples taken from along the H(2)S gradient in the outflow channel resulted in the isolation of an As(III)-oxidizing chemolithotroph from the low-H(2)S region of the gradient. The isolate was phylogenetically related to Acidicaldus and was characterized in vitro for spring-relevant properties, which were then compared to its distribution pattern in the spring as determined by denaturing gradient gel electrophoresis and quantitative PCR. While neither temperature nor oxygen requirements appeared to be related to the occurrence of this organism within the outflow channel, H(2)S concentration appeared to be an important constraint. This was verified by in vitro pure-culture modeling and kinetic experiments, which suggested that H(2)S inhibition of As(III) oxidation is uncompetitive in nature. In summary, the studies reported herein illustrate that H(2)S is a potent inhibitor of As(III) oxidation and will influence the niche opportunities and population distribution of As(III) chemolithotrophs.

Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage

Metal resistance determinants have traditionally been found in cultivated bacteria. To search for genes involved in nickel resistance, we analyzed the bacterial community of the rhizosphere of Erica andevalensis, an endemic heather which grows at the banks of the Tinto River, a naturally metal-enriched and extremely acidic environment in southwestern Spain. 16S rRNA gene sequence analysis of rhizosphere DNA revealed the presence of members of five phylogenetic groups of Bacteria and the two main groups of Archaea mostly associated with sites impacted by acid mine drainage (AMD). The diversity observed and the presence of heavy metals in the rhizosphere led us to construct and screen five different metagenomic libraries hosted in Escherichia coli for searching novel nickel resistance determinants. A total of 13 positive clones were detected and analyzed. Insights about their possible mechanisms of resistance were obtained from cellular nickel content and sequence similarities. Two clones encoded putative ABC transporter components, and a novel mechanism of metal efflux is suggested. In addition, a nickel hyperaccumulation mechanism is proposed for a clone encoding a serine O-acetyltransferase. Five clones encoded proteins similar to well-characterized proteins but not previously reported to be related to nickel resistance, and the remaining six clones encoded hypothetical or conserved hypothetical proteins of uncertain functions. This is the first report documenting nickel resistance genes recovered from the metagenome of an AMD environment.

Isolation, characterization, and ecology of sulfur-respiring crenarchaea inhabiting acid-sulfate-chloride-containing geothermal springs in Yellowstone National Park

Elemental sulfur (S(0)) is associated with many geochemically diverse hot springs, yet little is known about the phylogeny, physiology, and ecology of the organisms involved in its cycling. Here we report the isolation, characterization, and ecology of two novel, S(0)-reducing Crenarchaea from an acid geothermal spring referred to as Dragon Spring. Isolate 18U65 grows optimally at 70 to 72 degrees C and at pH 2.5 to 3.0, while isolate 18D70 grows optimally at 81 degrees C and pH 3.0. Both isolates are chemoorganotrophs, dependent on complex peptide-containing carbon sources, S(0), and anaerobic conditions for respiration-dependent growth. Glycerol dialkyl glycerol tetraethers (GDGTs) containing four to six cyclopentyl rings were present in the lipid fraction of isolates 18U65 and 18D70. Physiological characterization suggests that the isolates are adapted to the physicochemical conditions of Dragon Spring and can utilize the natural organic matter in the spring as a carbon and energy source. Quantitative PCR analysis of 16S rRNA genes associated with the S(0) flocs recovered from several acid geothermal springs using isolate-specific primers indicates that these two populations together represent 17 to 37% of the floc-associated DNA. The physiological characteristics of isolates 18U65 and 18D70 are consistent with their potential widespread distribution and putative role in the cycling of sulfur in acid geothermal springs throughout the Yellowstone National Park geothermal complex. Based on phenotypic and genetic characterization, the designations Caldisphaera draconis sp. nov. and Acidilobus sulfurireducens sp. nov. are proposed for isolates 18U65 and 18D70, respectively.

Seasonal and diel distributions of denitrifying and bacterial communities in a hypersaline microbial mat (Camargue, France)

Changes in spatio-temporal distribution of bacterial and denitrifying communities were qualitatively studied in a microbial mat from Camargue (France). During a diel and a seasonal cycle, patterns of 16S rRNA and nitrite reductase genes (nirS and nirK) were compared by denaturing gradient gel electrophoresis (DGGE). Statistical analysis of DGGE profiles showed a significant seasonal shift in the community structure of the nirS-containing bacteria with a winter superficial population that extended in summer, whereas the nirK-containing bacteria seemed more affected by vertical gradients rather than by month-to month-changes. Denitrifying activities remained stable during these sampling times. The bacterial community at the surface of the mat also changed according to season, but appeared stable over a day. Finally, during a diel cycle nirK populations were localized in zones with large fluctuations of environmental parameters (oxygen, pH, and sulfur levels) while nirS populations seemed more restricted to the permanent anoxic layer of the microbial mat.