Microbial manganese and sulfate reduction in Black Sea shelf sediments

The microbial ecology of anaerobic carbon oxidation processes was investigated in Black Sea shelf sediments from mid-shelf with well-oxygenated bottom water to the oxic-anoxic chemocline at the shelf-break. At all stations, organic carbon (Corg) oxidation rates were rapidly attenuated with depth in anoxically incubated sediment. Dissimilatory Mn reduction was the most important terminal electron-accepting process in the active surface layer to a depth of ∼1 cm, while SO42− reduction accounted for the entire Corg oxidation below. Manganese reduction was supported by moderately high Mn oxide concentrations. A contribution from microbial Fe reduction could not be discerned, and the process was not stimulated by addition of ferrihydrite. Manganese reduction resulted in carbonate precipitation, which complicated the quantification of Corg oxidation rates. The relative contribution of Mn reduction to Corg oxidation in the anaerobic incubations was 25 to 73% at the stations with oxic bottom water. In situ, where Mn reduction must compete with oxygen respiration, the contribution of the process will vary in response to fluctuations in bottom water oxygen concentrations. Total bacterial numbers as well as the detection frequency of bacteria with fluorescent in situ hybridization scaled to the mineralization rates. Most-probable-number enumerations yielded up to 105 cells of acetate-oxidizing Mn-reducing bacteria (MnRB) cm−3, while counts of Fe reducers were <102 cm−3. At two stations, organisms affiliated with Arcobacter were the only types identified from 16S rRNA clone libraries from the highest positive MPN dilutions for MnRB. At the third station, a clone type affiliated with Pelobacter was also observed. Our results delineate a niche for dissimilatory Mn-reducing bacteria in sediments with Mn oxide concentrations greater than ∼10 μmol cm−3 and indicate that bacteria that are specialized in Mn reduction, rather than known Mn and Fe reducers, are important in this niche

Review The species concept for prokaryotes

The species concept is a recurrent controversial issue that preoccupies philosophers as well as biologists of all disciplines. Prokaryotic species concept has its own history and results from a series of empirical improvements parallel to the development of the techniques of analysis. Among the microbial taxonomists, there is general agreement that the species concept currently in use is useful, pragmatic and universally applicable within the prokaryotic world. However, this empirically designed concept is not encompassed by any of the, at least, 22 concepts described for eukaryotes. The species could be described as ‘a monophyletic and genomically coherent cluster of individual organisms that show a high degree of overall similarity in many independent characteristics, and is diagnosable by a discriminative phenotypic property’. We suggest to refer it as a phylo‐phenetic species concept. Here, we discuss the validity of the concept in use which we believe is more pragmatic in comparison with those concepts described for eukaryotes

Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil

The bacterial diversity assessed from clone libraries prepared from rRNA (two libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated biphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Nearly 29% of the cloned sequences in the rDNA library were identical to sequences in the rRNA libraries. More than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a clone group with sequence similarity higher than 97% [98% for Burkholderia andPseudomonas-type clones]) represented in both types of libraries. Some of those phylogenetic groups, mostly represented by a single (or pair) of cloned sequence type(s), were observed in only one of the types of library. An important difference between the libraries was the lack of clones representative of the Actinobacteriain the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparent abundance of bacteria affiliated to the beta-subclass of theProteobacteria, and to the genus Burkholderiain particular, was confirmed by fluorescence in situ hybridization analysis. The possible influence on apparent diversity of low template concentrations was assessed by dilution of the RNA template prior to amplification by reverse transcription-PCR. Although differences in the composition of the two rRNA libraries obtained from high and low RNA concentrations were observed, the main components of the bacterial community were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this study

Technical note: Comparison of automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) to assess bacterial diversity in the rumen of sheep

The aim of this study was to compare automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) techniques to assess bacterial diversity in the rumen of sheep. Sheep were fed 2 diets with 70% of either alfalfa hay or grass hay, and the solid (SOL) and liquid (LIQ) phases of the rumen were sampled immediately before feeding (0 h) and at 4 and 8 h postfeeding. Both techniques detected similar differences between forages, with alfalfa hay promoting greater (P 0.05) over the postfeeding period were detected by DGGE. The ARISA technique showed lower (P 0.05) in bacterial diversity between both rumen phases were detected by DGGE. Under the conditions of this study, the DGGE was not sensitive enough to detect some changes in ruminal bacterial communities, and therefore ARISA was considered more accurate for assessing bacterial diversity of ruminal samples. The results highlight the influence of the fingerprinting technique used to draw conclusions on factors affecting ruminal bacterial diversity

SeqCode: a nomenclatural code for prokaryotes described from sequence data

Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.Funding was provided by the US National Science Foundation (DEB 1841658, DEB 1557042 and EAR 1516680) to B.H., A.-L.R. and A.M.; the US National Institute of General Medical Sciences (GM103440) from the National Institutes of Health to B.H.; the Spanish Ministry of Science, Innovation and Universities (PGC2018-096956-B-C41 and PID2021-126114NB-C42) to R.R.; the Australian Research Council (FL150100038) to P.H.; the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, SFB 1439/1 2021—426547801) and European Regional Development Funds (FEDER) to A.P.; and the International Society for Microbial Ecology (ISME) to all authors

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.Funding was provided by the US National Science Foundation (DEB 1841658 and EAR 1516680), the US National Institute of General Medical Sciences (P20 GM103440) from the National Institutes of Health, the Spanish Ministry of Science, Innovation and Universities (PID2021-126114NB-C42), the Australian Research Council (FL150100038), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, SFB 1439/1 2021 – 426547801) also supported with European Regional Development Funds (FEDER), and the International Society for Microbial Ecology (ISME

Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov.

The family Chlamydiaceae currently comprises a single genus Chlamydia, with 11 validly published species and seven more taxa. It includes the human pathogens Chlamydia (C.) trachomatis, C. pneumoniae and C. psittaci, a zoonotic agent causing avian chlamydiosis and human psittacosis, as well as other proven or potential pathogens in ruminants, birds, snakes, reptiles and turtles. During routine testing of 15 apparently healthy captive flamingos in a zoo in 2011, an atypical strain of Chlamydiaceae was detected by real-time PCR of cloacal swab samples. Sequence analysis of the 16S rRNA gene revealed high similarity to the uncultured Chlamydiales bacterium clone 122, which previously had been found in gulls. As more samples were collected during annual campaigns of the flamingo ringing program in southern France from 2012 to 2015, Chlamydiaceae-specific DNA was detected by PCR in 30.9% of wild birds. From these samples, three strains were successfully grown in cell culture. Ultrastructural analysis, comparison of 16S and 23S rRNA gene sequences, whole-genome analysis based on de novo hybrid-assembled sequences of the new strains as well as subsequent calculation of taxonomic parameters revealed that the relatedness of the flamingo isolates to established members of the family Chlamydiaceae was sufficiently distant to indicate that the three strains belong to two distinct species within a new genus. Based on these data, we propose the introduction of Chlamydiifrater gen. nov., as a new genus, and Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov., as two new species of the genus.Martin Hölzer appreciates the support of the Joachim Herz Foundation by the add-on fellowship for interdisciplinary life science.Peer reviewe

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization?

Aim Biogeographical regions are the fundamental geographical units for grouping Earth's biodiversity. Biogeographical regionalization has been demonstrated for many higher taxa, such as terrestrial plants and vertebrates, but not in microbial communities. Therefore, we sought to test empirically whether microbial communities, or taxa, show patterns consistent with biogeographical regionalization. Location Within halite (NaCl) crystals from coastal solar salterns of western Europe, the Mediterranean and east Africa. Time period Modern (2006–2013). Major taxa studied Archaea. Methods Using high-throughput Illumina amplicon sequencing, we generated the most high-resolution characterization of halite-associated archaeal communities to date, using samples from 17 locations. We grouped communities into biogeographical clusters based on community turnover to test whether these communities show biogeographical regionalization. To examine whether individual taxa, rather than communities, show biogeographical patterns, we also tested whether the relative abundance of individual genera may be indicative of a community's biogeographical origins using machine learning methods, specifically random forest classification. Results We found that the rate of community turnover was greatest over subregional spatial scales (< 500 km), whereas at regional spatial scales the turnover was independent of geographical distance. Biogeographical clusters of communities were either not statistically robust or lacked spatial coherence, inconsistent with biogeographical regionalization. However, we identified several archaeal genera that were good indicators of biogeographical origin, providing classification error rates of < 10%. Main conclusions Overall, our results provide little support for the concept of biogeographical regions in these extremophilic microbial communities, despite the fact that some taxa do show biogeographical patterns. We suggest that variable dispersal ability among the halite-associated Archaea may disrupt biogeographical patterns at the community level, preventing the formation of biogeographical regions. This means that the processes that lead to the formation of biogeographical regions operate differentially on individual microbial taxa rather than on entire communities