Showing papers in "Environmental Microbiology Reports in 2012"

Local and regional factors influencing bacterial community assembly

Abstract: The classical view states that microbial biogeography is not affected by dispersal barriers or historical events, but only influenced by the local contemporary habitat conditions (species sorting). This has been challenged during recent years by studies suggesting that also regional factors such as mass effect, dispersal limitation and neutral assembly are important for the composition of local bacterial communities. Here we summarize results from biogeography studies in different environments, i.e. in marine, freshwater and soil as well in human hosts. Species sorting appears to be the most important mechanism. However, this result might be biased since this is the mechanism that is easiest to measure, detect and interpret. Hence, the importance of regional factors may have been underestimated. Moreover, our survey indicates that different assembly mechanisms might be important for different parts of the total community, differing, for example, between generalists and specialists, and between taxa of different dispersal ability and motility. We conclude that there is a clear need for experimental studies, first, to clearly separate regional and local factors in order to study their relative importance, and second, to test whether there are differences in assembly mechanisms depending on different taxonomic or functional groups.

Bacterial communities in floral nectar.

Abstract: Summary Floral nectar is regarded as the most important reward available to animal-pollinated plants to attract pollinators. Despite the vast amount of publications on nectar properties, the role of nectar as a natural bacterial habitat is yet unexplored. To gain a better understanding of bacterial communities inhabiting floral nectar, culture-dependent and -independent (454-pyrosequencing) methods were used. Our findings demonstrate that bacterial communities in nectar are abundant and diverse. Using culture-dependent method we showed that bacterial communities of nectar displayed significant variation among three plant species: Amygdalus communis, Citrus paradisi and Nicotiana glauca. The dominant class in the nectar bacterial communities was Gammaproteobacteria. About half of the isolates were novel species (< 97% similarities of the 16S rRNA gene with known species). Using 454-pyrosequencing we demonstrated that nectar microbial community are distinct for each of the plant species while there are no significant differences between nectar microbial communities within nectars taken from different plants of the same species. Primary selection of the nectar bacteria is unclear; it may be affected by variations in the chemical composition of the nectar in each plant. The role of the rich and diverse nectar microflora in the attraction–repulsion relationships between the plant and its nectar consumers has yet to be explored.

Phylogenetic clustering increases with elevation for microbes.

Abstract: Summary Although phylogenetic approaches are useful for pro- viding insights into the processes underlying biodi- versity patterns, the studies of microbial phylogenetic relatedness are rare, especially for elevational gra- dients. Using high-throughput pyrosequencing, we examined the biodiversity patterns for biofilm bacte- rial communities that were scraped from stream stones along an elevational gradient from 1820 to 4050 m in China. The patterns of bacterial species richness and phylogenetic diversity were hollow towards higher elevations. The bacterial communities consisted of closer relatives than expected and dis- played increasing terminal phylogenetic clustering towards mountain top. The increasing phylogenetic clustering with elevation contrasts reports for macro- organisms that revealed phylogenetic overdispersion at low or intermediate elevations. Because water temperature showed the strongest correlation with phylogenetic relatedness (r 2 = 0.516), the elevational pattern in the bacterial phylogenetic structure indi- cated that environmental filtering possibly due to lower temperature or more frequent temperature fluc- tuations increased towards higher elevations. Evi- dence supporting the environmental filtering on bacteria was also reflected by the orderly succession in the relative abundance of different bacterial phyla along the elevational gradient and in the high even- ness of bacterial taxa at higher elevations. Overall, our results indicated that ecological processes pos- sibly related to temperature may play a dominant role in structuring bacterial biodiversity along the eleva- tional gradient.

Geomycology: metals, actinides and biominerals

Abstract: Geomycology can be simply defined as 'the scientific study of the roles of fungi in processes of fundamental importance to geology' and the biogeochemical importance of fungi is significant in several key areas. These include nutrient and element cycling, rock and mineral transformations, bioweathering, mycogenic biomineral formation and interactions of fungi with clay minerals and metals. Such processes can occur in aquatic and terrestrial habitats, but it is in the terrestrial environment where fungi probably have the greatest geochemical influence. Of special significance are the mutualistic relationships with phototrophic organisms, lichens (algae, cyanobacteria) and mycorrhizas (plants). Central to many geomycological processes are transformations of metals and minerals, and fungi possess a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Some fungal transformations have beneficial applications in environmental biotechnology, e.g. in metal and radionuclide leaching, recovery, detoxification and bioremediation, and in the production or deposition of biominerals or metallic elements with catalytic or other properties. Metal and mineral transformations may also result in adverse effects when these processes result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment. The ubiquity and importance of fungi in biosphere processes underlines the importance of geomycology as an interdisciplinary subject area within microbiology and mycology.

A genetic system for Geobacter metallireducens: role of the flagellin and pilin in the reduction of Fe(III) oxide

Abstract: Summary Geobacter metallireducens is an important model organism for many novel aspects of extracellular electron exchange and the anaerobic degradation of aromatic compounds, but studies of its physiology have been limited by a lack of techniques for gene deletion and replacement. Therefore, a genetic system was developed for G. metallireducens by making a number of modifications in the previously described approach for homologous recombination in Geobacter sulfurreducens. Critical modifications included, among others, a 3.5-fold increased in the quantity of electrotransformed linear DNA and the harvesting of cells at early-log. The Cre-lox recombination system was used to remove an antibiotic resistance cassette from the G. metallireducens chromosome permitting the generation of multiple mutations in the same strain. Deletion of the gene fliC, which encodes the flagellin protein, resulted in a strain that did not produce flagella, was non-motile, and was defective for the reduction of insoluble Fe(III). Deletion of pilA, which encodes the structural protein of the type IV pili, inhibited the production of lateral pili as well as Fe(III) oxide reduction and electron transfer to an electrode. These results demonstrate the importance of flagella and pili in the reduction of insoluble Fe(III) by G. metallireducens and provide methods for additional genetic-based approaches for the study of G. metallireducens.

Macroecology of unicellular organisms – patterns and processes

Abstract: Summary Macroecology examines the relationship between organisms and their environment at large spatial (and temporal) scales. Typically, macroecologists explain the large-scale patterns of abundance, distribution and diversity. Despite the difficulties in sampling and characterizing microbial diversity, macroecologists have recently also been interested in unicellular organisms. Here, I review the current advances made in microbial macroecology, as well as discuss related ecosystem functions. Overall, it seems that microorganisms suit surprisingly well to known species abundance distributions and show positive relationship between distribution and adundance. Microbial species–area and distance–decay relationships tend to be weaker than for macroorganisms, but nonetheless significant. Few findings on altitudinal gradients in unicellular taxa seem to differ greatly from corresponding findings for larger taxa, whereas latitudinal gradients among microorganisms have either been clearly evident or absent depending on the context. Literature also strongly emphasizes the role of spatial scale for the patterns of diversity and suggests that patterns are affected by species traits as well as ecosystem characteristics. Finally, I discuss the large role of local biotic and abiotic variables driving the community assembly in unicellular taxa and eventually dictating how multiple ecosystem processes are performed. Present review highlights the fact that most microorganisms may not differ fundamentally from larger taxa in their large-scale distribution patterns. Yet, review also shows that many aspects of microbial macroecology are still relatively poorly understood and specific patterns depend on focal taxa and ecosystem concerned.

Which sequencing depth is sufficient to describe patterns in bacterial α‐ and β‐diversity?

Abstract: The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may th ...

Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome.

Abstract: Summary Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder in western coun- tries. Previous studies on IBS, mostly based on faecal samples, suggest alterations in the intestinal micro- biota. However, no consensus has been reached regarding the association between specific bacteria and IBS. We explore the alterations of intestinal bac- terial communities in IBS using massive sequencing of amplified 16S rRNA genes. Mucosal biopsies of the ascending and descending colon and faeces from 16 IBS patients and 9 healthy controls were analysed. Strong inter-individual variation was observed in the composition of the bacterial communities in both patients and controls. These communities showed less diversity in IBS cases. There were larger differ- ences in the microbiota composition between biop- sies and faeces than between patients and controls. We found a few over-represented and under-

Abundance of anammox bacteria in different wetland soils

Abstract: Summary The diversity and activity of anammox bacteria has been studied in various environments, but knowledge about their abundance and population dynamics is scarce and particularly lacking for soils. A SYBR Green qPCR protocol was developed for the quantification of anammox bacterial 16S rRNA gene copies using newly designed primers. This primer set allows specific detection of all currently known anammox candidate genera including members of a new anammox cluster. Seven wetland soils were investigated and anammox bacterial 16S rRNA gene copy numbers of 4.01 × 104 to 6.74 × 106 per gram of fresh soil were detected. Anammox bacteria were also quantified along a Gleysol profile at three different sampling dates. Anammox 16S rRNA gene abundance increased significantly with soil depth and varied only little between seasons, suggesting that anammox bacteria represent a minor but stable microbial population in this soil.

Abundant and diverse endophytic actinobacteria associated with medicinal plant Maytenus austroyunnanensis in Xishuangbanna tropical rainforest revealed by culture‐dependent and culture‐independent methods

Abstract: Endophytes are now considered as an important component of biodiversity. However, the diversity of endophytic actinobacteria associated with tropical rainforest native medicinal plants is essentially unknown. In this study, the diversity of endophytic actinobacteria residing in root, stem and leaf tissues of medicinal plant Maytenus austroyunnanensis collected from tropical rainforest in Xishuangbanna, China was investigated with a combination of cultivation and culture-independent analysis on the basis of 16S rRNA gene sequencing. By using different selective isolation media and methods, a total of 312 actinobacteria were obtained, and they were affiliated with the order Actinomycetales (distributed into 21 genera). Based on a protocol for endophytes enrichment, three 16S rRNA gene clone libraries were constructed and 84 distinct operational taxonomic units were identified and they distributed among the orders Actinomycetales and Acidimicrobiales, including eight suborders and at least 38 genera with a number of rare actinobacteria genera. Phylogenetic analysis showed that 32% of the clones in the libraries had lower than 97% similarities with related type strains. Interestingly, six genera from the order Actinomycetales and uncultured clones from Acidimicrobiales have not, to our knowledge, been previously reported as endophytes. Our study confirms abundant endophytic actinobacterial consortium in tropical rainforest native plant and suggests that this special habitat represents an underexplored reservoir of diverse and novel actinobacteria of potential interest for bioactive compounds discovery.

Colony collapse disorder in Europe

Abstract: Colony collapse disorder (CCD) is a condition of honey bees, which has contributed in part to the recent major losses of honey bee colonies in the USA. Here we report the first CCD case from outside of the USA. We suggest that more standardization is needed for the case definition to diagnose CCD and to compare data on a global scale.

Distribution and diversity of anaerobic ammonium-oxidizing bacteria in the sediments of the Qiantang River.

Abstract: Anaerobic ammonium oxidation (anammox) is an important process in the marine nitrogen cycle. However, little is known about the distribution, diversity and abundance of anammox bacteria in inland river ecosystems. Here, we found the presence of diverse anammox bacteria in a freshwater river - the Qiantang River, Zhejiang Province (China). The phylogenetic analysis of 16S rRNA genes showed that Brocadia genus, Kuenenia genus, Scalindua genus and three new anammox bacterial clusters could be detected together in Qiantang River sediments, suggesting a higher anammox bacterial diversity in the Qiantang River ecosystem than in open ocean environments where only Scalindua genus was detected. Brocadia and Kuenenia appeared to be the most common anammox bacterial genera in the Qiantang River. Redundancy analysis showed that the sediment organic carbon (OrgC) content had significant influence on the distribution of anammox bacteria in Qiantang River sediments. Pearson correlation analyses showed that OrgC content significantly influenced the anammox bacterial diversity. The results of real-time quantitative PCR showed spatial variations of anammox bacterial abundances which were highly correlated with the sediment total inorganic nitrogen content. These results demonstrated the distribution of diverse anammox bacteria and the influences of environmental factors on anammox bacterial communities in Qiantang River sediments.

Bacterial anoxygenic photosynthesis on plant leaf surfaces

Abstract: The aerial surface of plants, the phyllosphere, is colonized by numerous bacteria displaying diverse metabolic properties that enable their survival in this specific habitat. Recently, we reported on the presence of microbial rhodopsin harbouring bacteria on the top of leaf surfaces. Here, we report on the presence of additional bacterial populations capable of harvesting light as a means of supplementing their metabolic requirements. An analysis of six phyllosphere metagenomes revealed the presence of a diverse community of anoxygenic phototrophic bacteria, including the previously reported methylobacteria, as well as other known and unknown phototrophs. The presence of anoxygenic phototrophic bacteria was also confirmed in situ by infrared epifluorescence microscopy. The microscopic enumeration correlated with estimates based on metagenomic analyses, confirming both the presence and high abundance of these microorganisms in the phyllosphere. Our data suggest that the phyllosphere contains a phylogenetically diverse assemblage of phototrophic species, including some yet undescribed bacterial clades that appear to be phyllosphere-unique.

Dissemination of wine-related yeasts by migratory birds.

Abstract: Summary The present work was undertaken to evaluate the contribution of migratory birds in the environmental dissemination of yeasts. Four sites (Mazara del Vallo, Lampedusa, Ustica and Linosa), representing the main stop-over points in Sicily, were analysed during spring and autumnal bird migration and 349 birds (belonging to 10 families) were ringed and analysed for yeast presence. A total of 125 yeasts were isolated and identified by a multiple genotypic approach, consisting of restriction fragment length polymorphism (RFLP) of 5.8S rRNA gene and 26S rRNA and sequencing of D1/D2 domain of the 26S rRNA gene, which resulted in the recognition of 18 species, including the technological relevant Saccharomyces cerevisiae which were characterized at strain level applying three techniques (interdelta analysis, minisatellite analysis based on the separate amplification of three genes and microsatellite multiplex PCR of polymorphic microsatellite loci). The evaluation of the persistence of living S. cerevisiae in birds for about 12 h from ingestion of inoculated feed allowed the conclusion that yeasts with technological potential are disseminated during migration.

High cyanobacterial nifH gene diversity in Arctic seawater and sea ice brine.

Abstract: Although cyanobacterial diazotrophs are common in Arctic terrestrial and freshwater habitats, they have been assumed to be absent from Arctic marine habitats. We report here a high diversity of cyanobacterial nifH genes in Fram Strait and the Greenland Sea. The nifH gene encodes the iron protein of the nitrogenase enzyme complex, which is essential for biological N2 fixation. Using primers specific for nifH genes we uncovered communities of autotrophic and heterotrophic bacteria in sea ice brine and seawater between latitudes 65 and 81°N. Cyanobacteria (Oscillatoriales and Chroococcales) with known marine planktonic and benthic distributions were distinguished, alongside a mix of metabolically versatile eubacteria (nifH Clusters I and III). Using primers selective for cyanobacterial nifH genes we identified filamentous non-heterocystous Trichodesmium-like and LPP (Leptolyngbya, Phormidium and Plectonema)-like Oscillatoriales, as well as Cyanothece-like Chroococcales in a brine sample from 81°N. The occurrence of Trichodesmium-like cyanobacteria was further confirmed by sequences of the hetR gene of Trichodesmium. Microscopic examinations confirmed the presence of viable filamentous and unicellular cyanobacteria. Our results reveal the potential for microbial N2 fixation in the Arctic seas. However, it is still left to determine if these genes are also metabolically active before any biogeochemical importance of diazotrophy in the polar oceans can be assessed.

Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in co-culture with Sedimentibacter sp.

Abstract: Summary The importance of Dehalobacter species in bioremediation as dedicated degraders of chlorinated organics has been well recognized. However, still little is known about Dehalobacter's full genomic repertoires, including the genes involved in dehalogenation. Here we report the first insights into the genome sequence of Dehalobacter sp. E1 that grows in strict co-culture with Sedimentibacter sp. B4. Based on the co-culture metagenome and the genome of strain B4 (4.2 Mbp) we estimate the genome sequence of strain E1 to be 2.6 Mbp. Ten putative reductive dehalogenase homologue (Rdh)-encoding gene clusters were identified. One cluster has a putative tetrachloroethene Rdh-encoding gene cluster, similar to the pceABCT operon previously identified in Dehalobacter restrictus. Metagenome analysis indicated that the inability of strain E1 to synthesize cobalamin, an essential cofactor of reductive dehalogenases, is complemented by Sedimentibacter. The metagenomic exploration described here maps the extensive dechlorinating potential of Dehalobacter, and paves way for elucidation of the interactions with its co-cultured Sedimentibacter.

Cholesterol metabolism in Mycobacterium smegmatis

Abstract: Summary The metabolism of cholesterol in Mycobacterium smegmatis mc2155 has been investigated by using a microarray approach. The transcriptome of M. smegmatis growing in cholesterol was compared with that of cells growing in glycerol as the sole carbon and energy sources during the middle exponential phase. Microarray analyses revealed that only 89 genes were upregulated at least threefold during growth on cholesterol compared with growth on glycerol. The upregulated genes are scattered throughout the 7 Mb M. smegmatis genome and likely reflect a general physiological adaptation of the bacterium to grow on this highly hydrophobic polycyclic compound. Nevertheless, 39 of the catabolic genes are organized in three specific clusters. These results not only supported the role of KstR and KstR2 as auto-regulated repressors of cholesterol catabolism, and revealed some metabolic similarities and differences on actinobacteria, but more important, they have facilitated the identification of new catabolic genes, opening a research scenario that might provide important clues on the role of cholesterol in tuberculosis infection.

Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC

Abstract: Summary Free-living Actinobacteria are universally recognized as high-GC organisms. Freshwater Actinobacteria have been identified as abundant and prevalent members of freshwater microbial communities, but the two most common lineages (acI and acIV) have remained impossible to culture to date. We have analysed metagenomic data from lakes and estuaries, and show that members of acI and acIV are indeed abundant. We then show that the majority of actinobacterial reads from metagenomic datasets (both lakes and estuaries) are consistently low GC. Analysis of assembled scaffolds from these datasets also confirms that actinobacterial scaffolds are primarily low GC, although high-GC scaffolds were also observed, indicating both types of Actinobacteria coinhabit. Phylogenetic analysis of 16S rRNA gene sequences, both from PCR-based clone libraries and metagenomic reads, and the discovery of a low-GC scaffold containing a partial 16S rRNA gene, points to the abundance of the well-known acI and acIV lineages of freshwater in these habitats, both of which appear to be low GC.

Nitrous oxide production in soil isolates of nitrate-ammonifying bacteria.

Abstract: Here we provide the first demonstration of the potential for N2O production by soil-isolated nitrate-ammonifying bacteria under different C and N availabilities, building on characterizations informed from model strains. The potential for soil-isolated Bacillus sp. and Citrobacter sp. to reduce NO3-, and produce NH4+, NO2- and N2O was examined in batch and continuous (chemostat) cultures under different C-to-NO3- ratios, NO3--limiting (5 mM) and NO3--sufficient (22 mM) conditions. C-to-NO3- ratio had a major influence on the products of nitrate ammonification, with NO2-, rather than NH4+, being the major product at low C-to-NO3- ratios in batch cultures. N2O production was maximum and accompanied by high NO2- production under C-limitation/NO3-sufficiency conditions in chemostat cultures. In media with lower C-to-NO3-N ratios (5- and 10-to-1) up to 2.7% or 5.0% of NO3- was reduced to N2O by Bacillus sp. and Citrobacter sp., respectively, but these reduction efficiencies were only 0.1% or 0.7% at higher C-to-NO3- ratios (25- and 50-to-1). As the highest N2O production did not occur under the same C-to-NO3- conditions as highest NH4+ production we suggest that a re-evaluation may be necessary of the environmental conditions under which nitrate ammonification contributes to N2O emission from soil.

Age, sun and substrate: triggers of bacterial communities in lichens

Abstract: Summary Bacterial communities colonize the surfaces of lichens in a biofilm-like manner. The overall structure of the bacterial communities harboured by the lichens shows similarities, in particular the dominance of not yet cultured Alphaproteobacteria. Parameters causing variation in abundance, composition and spatial organization of the lichen-associated bacterial communities are so far poorly understood. As a first step, we used a microscopic approach to test the significance of both lichen-intrinsic and extrinsic environmental factors on the bacterial communities associated with 11 lichen samples, belonging to six species. Some of these species have thalli with a distinct age gradient. A statistically significant effect can be attributed to the age of the thallus parts, which is an intrinsic factor: growing parts of the lichens host bacterial communities that significantly differ from those of the ageing portions of the thalli. The substrate type (rock, tree, understory) and (at a lower extent) the exposition to the sun also affected the bacterial communities. Interestingly, the abundance of bacterial cells in the lichens was also influenced by the same structure-triggering factors. No effect on the composition with main bacterial groups was attributed to different lichen species, differentiated thallus parts or thallus growth type. Our results are important for the experimental designs in lichen-bacterial ecology.

Highly divergent Staphylococcus aureus isolates from African non‐human primates

Abstract: Summary Staphylococcus aureus is a bacterium that colonizes and infects both humans and animals. As little is known about the phenotypic and molecular characteristics of S. aureus from wild animals in sub-Saharan Africa, the objective of the study was to characterize S. aureus isolates from wildlife and to analyse if they differed from those found among humans. The resistance to penicillin was low in S. aureus isolates from non-human primates (2.9%). Phylogenetic analysis based on the concatenated sequences from multilocus sequence typing revealed two highly divergent groups of isolates. One group was predominated by S. aureus that belonged to known human-related STs (ST1, ST9 and ST601) and mainly derived from great apes. A second clade comprised isolates with novel STs. These isolates were different from classical human S. aureus strains and mainly derived from monkeys. Our findings provide the basis for future studies addressing the inter- and intra-species transmission of S. aureus in Africa.

Different strategies in anaerobic biodegradation of aromatic compounds : nitrate reducers versus strict anaerobes

Abstract: Summary Mononuclear aromatic compounds are degraded anaerobically through pathways that are basically different from those used in the presence of oxygen. Whereas aerobic degradation destabilizes the aromatic π-electron system by oxidative steps through oxygenase reactions, anaerobic degradation is most often initiated by a reductive attack. The benzoyl-CoA pathway is the most important metabolic route in this context, and a broad variety of mononuclear aromatics, including phenol, cresols, toluene, xylenes and ethylbenzene, are channelled into this pathway through various modification reactions. Multifunctional phenolic compounds are metabolized via the reductive resorcinol pathway, the oxidative resorcinol pathway with hydroxyhydroquinone as key intermediate, and the phloroglucinol pathway. Comparison of the various pathways used for modification and degradation of aromatics in the absence of oxygen indicates that the strategies of breakdown of these compounds are largely determined by the redox potentials of the electron acceptors used, and by the overall reaction energetics. Consequently, nitrate reducers quite often use strategies for primary attack on aromatic compounds that differ from those used by sulfate-reducing, iron-reducing or fermenting bacteria.

Differential responses of nirK- and nirS-carrying bacteria to denitrifying conditions in the anoxic rice field soil.

Abstract: Summary Denitrification occurs actively in rice field soils. In the present study, the responses of nirK and nirS denitrifier communities to nitrate addition in the anoxic rice soil were determined through molecular analyses of nitrite reductase genes nirK and nirS and 16S rRNA genes. Denitrification occurred rapidly when nitrate was added at the beginning of anoxic incubation (experiment I). The structure of nirK-type denitrifiers did not change; but their abundance as determined by quantitative (real-time) PCR increased in nitrate treatments compared with control. Both the structure and abundance of nirS denitrifiers remained unaffected in experiment I. The rate of denitrification was slowed down when nitrate was added 20 days after the onset of anoxic incubation (experiment II). The structure and abundance of nirK-type denitrifier community did not respond to nitrate addition; but the nirS community changed substantially in this experiment. The copy number of nirS genes increased by an order of magnitude in the treatments of 5 mM and 10 mM nitrate compared with control. The terminal restriction fragment length polymorphism (T-RFLP) analysis of nirS genes revealed that the 100 bp T-RF substantially increased in the nitrate treatments. Cloning and sequence analysis indicated that this T-RF had similarity of up to 90% with Herbaspirillum sp. T-RFLP profiles of the bacterial 16S rRNA genes also showed that Herbaspirillum sp. increased after nitrate amendments. Collectively, the nirK-type denitrifiers were probably active at the beginning of anaerobic incubation, while the nirS denitrifiers, especially those related with Herbaspirillum sp. probably were more active when anaerobic condition was fully developed.

Unsuspected control of siderophore production by N‐acetylglucosamine in streptomycetes

Abstract: Summary Iron is one of the most abundant elements on earth but is found in poorly soluble forms hardly accessible to microorganisms. To subsist, they have developed iron-chelating molecules called siderophores that capture this element in the environment and the resulting complexes are internalized by specific uptake systems. While biosynthesis of siderophores in many bacteria is regulated by iron availability and oxidative stress, we describe here a new type of regulation of siderophore production. We show that in Streptomyces coelicolor, their production is also controlled by N-acetylglucosamine (GlcNAc) via the direct transcriptional repression of the iron utilization repressor dmdR1 by DasR, the GlcNAc utilization regulator. This regulatory nutrient–metal relationship is conserved among streptomycetes, which indicates that the link between GlcNAc utilization and iron uptake repression, however unsuspected, is the consequence of a successful evolutionary process. We describe here the molecular basis of a novel inhibitory mechanism of siderophore production that is independent of iron availability. We speculate that the regulatory connection between GlcNAc and siderophores might be associated with the competition for iron between streptomycetes and their fungal soil competitors, whose cell walls are built from the GlcNAc-containing polymer chitin. Alternatively, GlcNAc could emanate from streptomycetes’ own peptidoglycan that goes through intense remodelling throughout their life cycle, thereby modulating the iron supply according to specific needs at different stages of their developmental programme.

Environment may be the source of Flavobacterium columnare outbreaks at fish farms

Abstract: Summary Flavobacterium columnare, causing columnaris disease, was isolated for the first time from free water and biofilms in the environment outside fish farms. Fourteen isolates were found from Central Finland from a river by a water intake of a salmonid farm and 400 m upstream of the farm. One isolate was from a lake not under the influence of any fish farming. The bacterium could not be isolated from five other lakes in Central Finland or from three lakes in Eastern Finland, none of them in use for fish farming. Among the environmental isolates there was both genetic variability and difference in virulence, but the isolates were less virulent than the isolates originating from a disease outbreak at a fish farm. The isolates were able to survive for months outside the fish host and also to change their colony morphology, a phenomenon probably used as a survival strategy for F. columnare. This indicates that waters upstream of fish farms are a potential source of columnaris outbreaks at the farms during the summer. The results support the hypothesis that fish farms and farming practices may select for the virulent strains of F. columnare occurring in environmental waters to cause the infections at the farms.

Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study.

Abstract: Summary The extent to which different sequence-based approaches describe environmental microbial communities in comparative studies is an important consideration when deriving inferences from ecological studies. The ability of a targeted metagenomic approach [small subunit (SSU) rRNA pyrosequencing] and shotgun metagenome approaches were compared to identify distinguishing features in dryland soil microbial communities from two different habitats: biological soil crusts (biocrusts) and creosote bush root zones. A parallel comparison was conducted to determine the ability of each approach to detect community differences potentially arising from a more subtle experimental treatment, long-term elevated atmospheric carbon dioxide. As expected, the biocrust datasets were clearly differentiated from root zone datasets using either of the sequencing approaches. However, the composition described by each approach was significantly different. The magnitude of comparative differences due to habitat or elevated CO2 treatment was larger with pyrosequenced SSU datasets or SSU reads recruited from shotgun metagenomes, than from SEED-classified shotgun metagenome reads. Finally, based on prior knowledge of the biocrust communities, the SSU-based datasets more accurately identified the dominant biocrust cyanobacteria sequences compared to the shotgun metagenome datasets.

The temporal dynamics of bacterial communities across human anterior nares.

Abstract: The anterior nares (nostrils), are an important niche for bacterial colonization by both commensals and opportunistic pathogens. Here the temporal dynamics and variation of the global nasal bacterial community across 25 healthy volunteers was evaluated over 15 months. Overall, there was a global seasonal shift in bacterial community structure. Such a temporal shift was also strongly evident in the abundances of species such as Propionibacterium acnes and Staphylococcus epidermidis. However, such species dynamics over time was also inter-individual-dependent, and both individuals with highly stable communities and those with highly flexible communities could be defined. Even though the bacterial community of individual volunteers was thus generally variable over time and permanent carriage of a given species was seldomly observed, various species previously defined as constituting the core bacterial community could be identified as persistent in a subset of the volunteers suggesting that these same species also constitute to a 'temporal' core community.

Sub-inhibitory concentrations of different pharmaceutical products affect the meta-transcriptome of river biofilm communities cultivated in rotating annular reactors.

Abstract: Summary Surface waters worldwide are contaminated by pharmaceutical products that are released into the environment from wastewater treatment plants. Here, we hypothesize that pharmaceutical products have effects on organisms as well as genes related to nutrient cycling in complex microbial communities. To test this hypothesis, biofilms were grown in reactors and subjected low concentrations of three antibiotics [erythromycin, ER, sulfamethoxazole, SL and sulfamethazine, SN) and a lipid regulator (gemfibrozil, GM). Total community RNA was extracted and sequenced together with PCR amplicons of the 16S rRNA gene using 454 pyrosequencing. Exposure to pharmaceutical products resulted in very little change in bacterial community composition at the phylum level based on 16S rRNA gene amplicons, even though some genera were significantly affected. In contrast, large shifts were observed in the active community composition based on taxonomic affiliations of mRNA sequences. Consequently, expression of gene categories related to N, P and C cycling were strongly affected by the presence of pharmaceutical products, with each treatment having specific effects. These results indicate that low pharmaceutical product concentrations rapidly provoke a variety of functional shifts in river bacterial communities. In the longer term these shifts in gene expression and microbial activity could lead to a disruption of important ecosystem processes like nutrient cycling.

Role of GbpA protein, an important virulence‐related colonization factor, for Vibrio cholerae's survival in the aquatic environment

Abstract: Summary Vibrio cholerae N-acetyl glucosamine-binding protein A (GbpA) is a chitin binding protein and a virulence factor involved in the colonization of human intestine. We investigated the distribution and genetic variations of gbpA in 488 V. cholerae strains of environmental and clinical origin, belonging to different serogroups and biotypes. We found that the gene is consistently present and highly conserved including an environmental V. cholerae-related strain of ancestral origin. The gene was also consistently expressed in a number of representative V. cholerae strains cultured in laboratory aquatic microcosms under conditions simulating those found in temperate marine environments. Functional analysis carried out on V. cholerae O1 El Tor N16961 showed that GbpA is not involved in adhesion to inorganic surfaces but promotes interaction with environmental biotic substrates (plankton and bivalve hepatopancreas cells) representing known marine reservoir or host for the bacterium. It is suggested that the ability of GbpA to colonize human intestinal cells most probably originated from its primary function in the aquatic environment.

The genome and transcriptome of a newly described psychrophilic archaeon, Methanolobus psychrophilus R15, reveal its cold adaptive characteristics.

Abstract: We analysed the cold-responsive gene repertoire for a psychrophilic methanogen, Methanolobus psychrophilus R15 through genomic and RNA-seq assayed transcriptomic comparisons for cultures at 18°C (optimal temperature) versus 4°C. The differences found by RNA-seq analysis were verified using quantitative real time-PCR assay. The results showed that as in the Antarctic methanogen, Methanococcoides burtonii, genes for methanogenesis, biosynthesis and protein synthesis were all downregulated by the cold in R15. However, the RNA polymerase complex was upregulated at cold, as well as a gene cluster for a putative exosome complex, suggesting that exosome-mediated RNA decay may be cold-accelerated. Unexpectedly, the chaperonin genes for both thermosome and GroES/EL were all upregulated at 4°C. Strain R15 possessed eight protein families for oxygen detoxification, including both anaerobe-specific superoxide reductase (SOR) and the aerobe-typical superoxide dismutase (SOD)-catalase oxidant-removing system, implying the higher oxidative tolerance. Compared with a mesophilic methanogen, R15 survived in higher paraquat, a redox-cycling drug. Moreover, 71 one-component systems and 50 two-component systems for signal transduction ranked strain R15, together with M. burtonii, as being highly adaptive among archaea. Most of them exhibited cold-enhanced expression, indicating their involvement in cold adaptation. This study has added new perspectives on the cold adaptation of methanogenic archaea.