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Metagenomics of marine sediments has uncovered a broad diversity of new uncultured taxa, and provided the insights into their metabolic capabilities. Here, we detected microbial lineages from a sediment core near the Jiulong methane reef of the northern South China Sea (at 1100 m depth). Assembly and binning of the metagenomes resulted in 11 genomes (>85% complete) that represented nine distinct phyla including candidate phyla TA06 and LCP-89, Lokiarchaeota, Heimdallarchaeota, and a newly described globally distributed phylum (B38). The genome of LCP-89 has pathways for nitrate, selenate and sulfate reduction, suggesting that they may be involved in mediating these important processes. The B38 is able to participate in the cycling of hydrogen and selenocompounds. Many of these uncultured microbes may also be capable of autotrophic CO2 fixation, as exemplified by identification of the Wood-Ljungdahl (W-L) pathway. The carbohydrate degradation, W-L pathway, Rnf-dependent energy conservation and Ni/Fe hydrogenases were detected in the transcriptomes of these novel members. Characterizations of these new lineages provide insights to the undescribed branches in the tree of life. IMPORTANCE Sedimentary microorganisms in the South China Sea (SCS) remain largely unknown, due to the complexity of sediment communities impacted by continent rifting and extension. Distinct geochemical environments may breed special microbial communities including microbes that are still enigmatic. Functional inference of their metabolisms and transcriptional activity provided the insights in the ecological roles and substrate-based interactivity of these uncultured Archaea and Bacteria. These microorganisms play different roles in utilizing inorganic carbon and scavenging diverse organic compounds to involve in deep-sea carbon cycle. The genomes recovered here contributed undescribed species to the tree of life and laid a foundation for future study on these novel phyla persisting in marginal sediments of the SCS. [ABSTRACT FROM AUTHOR]

Investigations of the biogeochemical roles of benthic A rchaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group ( MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-C oA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment. [ABSTRACT FROM AUTHOR]

Native speech perception is generally assumed to be highly efficient and accurate. Very little research has, however, directly examined the limitations of native perception, especially for contrasts that are only minimally differentiated acoustically and articulatorily. Here, we demonstrate that native speech perception may indeed be more difficult than is often assumed, where phonemes are highly similar, and we address the nature and extremes of consonant perception. We present two studies of native and non-native (English) perception of the acoustically and articulatorily similar four-way coronal stop contrast /t ʈ ȶ/ (apico-alveolar, apico-retroflex, lamino-dental, lamino-alveopalatal) of Wubuy, an indigenous language of Australia. The results show that all listeners find contrasts involving /ȶ/ easy to discriminate, but that, for both groups, contrasts involving /t ʈ / are much harder. Where the two groups differ, the results largely reflect native language (Wubuy vs English) attunement as predicted by the Perceptual Assimilation Model [, , ]. We also observe striking perceptual asymmetries in the native listeners' perception of contrasts involving the latter three stops, likely due to the differences in input frequency. Such asymmetries have not previously been observed in adults, and we propose a novel Natural Referent Consonant Hypothesis to account for the results. [ABSTRACT FROM AUTHOR]

The deep ocean is an important component of global biogeochemical cycles because it contains one of the largest pools of reactive carbon and nitrogen on earth. However, the microbial communities that drive deep-sea geochemistry are vastly unexplored. Metatranscriptomics offers new windows into these communities, but it has been hampered by reliance on genome databases for interpretation. We reconstructed the transcriptomes of microbial populations from Guaymas Basin, in the deep Gulf of California, through shotgun sequencing and de novo assembly of total community RNA. Many of the resulting messenger RNA (mRNA) contiguous sequences contain multiple genes, reflecting co-transcription of operons, including those from dominant members. Also prevalent were transcripts with only limited representation (2.8 times coverage) in a corresponding metagenome, including a considerable portion (1.2 Mb total assembled mRNA sequence) with similarity (96%) to a marine heterotroph, Alteromonas macleodii. This Alteromonas and euryarchaeal marine group II populations displayed abundant transcripts from amino-acid transporters, suggesting recycling of organic carbon and nitrogen from amino acids. Also among the most abundant mRNAs were catalytic subunits of the nitrite oxidoreductase complex and electron transfer components involved in nitrite oxidation. These and other novel genes are related to novel Nitrospirae and have limited representation in accompanying metagenomic data. High throughput sequencing of 16S ribosomal RNA (rRNA) genes and rRNA read counts confirmed that Nitrospirae are minor yet widespread members of deep-sea communities. These results implicate a novel bacterial group in deep-sea nitrite oxidation, the second step of nitrification. This study highlights metatranscriptomic assembly as a valuable approach to study microbial communities. [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing Archaea (AOA) are among the most abundant microorganisms in the oceans and have crucial roles in biogeochemical cycling of nitrogen and carbon. To better understand AOA inhabiting the deep sea, we obtained community genomic and transcriptomic data from ammonium-rich hydrothermal plumes in the Guaymas Basin (GB) and from surrounding deep waters of the Gulf of California. Among the most abundant and active lineages in the sequence data were marine group I (MGI) Archaea related to the cultured autotrophic ammonia-oxidizer, Nitrosopumilus maritimus. Assembly of MGI genomic fragments yielded 2.9 Mb of sequence containing seven 16S rRNA genes (95.4-98.4% similar to N. maritimus), including two near-complete genomes and several lower-abundance variants. Equal copy numbers of MGI 16S rRNA genes and ammonia monooxygenase genes and transcription of ammonia oxidation genes indicates that all of these genotypes actively oxidize ammonia. De novo genomic assembly revealed the functional potential of MGI populations and enhanced interpretation of metatranscriptomic data. Physiological distinction from N. maritimus is evident in the transcription of novel genes, including genes for urea utilization, suggesting an alternative source of ammonia. We were also able to determine which genotypes are most active in the plume. Transcripts involved in nitrification were more prominent in the plume and were among the most abundant transcripts in the community. These unique data sets reveal populations of deep-sea AOA thriving in the ammonium-rich GB that are related to surface types, but with key genomic and physiological differences. [ABSTRACT FROM AUTHOR]

The present study investigates the acoustic differentiation of three coronal stops in the indigenous Australian language Wubuy. We test independent claims that only VC (vowel-into-consonant) transitions provide robust acoustic cues for retroflex as compared to alveolar and dental coronal stops, with no differentiating cues among these three coronal stops evident in CV (consonant-into-vowel) transitions. The four-way stop distinction /t, t̪, ʈ, c/ in Wubuy is contrastive word-initially (Heath 1984) and by implication utterance-initially, i.e., in CV-only contexts, which suggests that acoustic differentiation should be expected to occur in the CV transitions of this language, including in initial positions. Therefore, we examined both VC and CV formant transition information in the three target coronal stops across VCV (word-internal), V#CV (word-initial but utterance-medial) and ##CV (word- and utterance-initial), for /а/ vowel contexts, which provide the optimal environment for investigating formant transitions. Results confirm that these coronal contrasts are maintained in the CVs in this vowel context, and in all three positions. The patterns of acoustic differences across the three syllable contexts also provide some support for a systematic role of prosodic boundaries in influencing the degree of coronal stop differentiation evident in the vowel formant transitions. [ABSTRACT FROM AUTHOR]

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledgeȓparticularly for Archaeaȓthat occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete ∼1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasma tales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISMEJ 3:159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren-and Euryarchaeotal lineages diverged. [ABSTRACT FROM AUTHOR]

Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain (northern California). Phylogenetic analysis revealed that the majority (68%) of the sequences belonged to fungi. Protists falling into the deeply branching lineage named the acidophilic protist clade (APC) and the class Heterolobosea were also present. The APC group represents kingdom-level novelty, with <76% sequence similarity to 18S rRNA gene sequences of organisms from other environments. Fluorescently labeled oligonucleotide rRNA probes were designed to target each of these groups in biofllm samples, enabling abundance and morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels. [ABSTRACT FROM AUTHOR]

Fully understanding the biology of acid mine drainage (AMD) is central to our ability to control and manipulate its environmental impact. Although genomics and biogeochemical methods are relatively well established in the field, their combination with high-resolution imaging of intact members of microbial biofilm communities has not yet reached its full potential. Here, we used three-dimensional (3D) cryogenic electron tomography to determine the size and ultrastructure of intact ARMAN cells, a novel ultra-small archaeon, and sought evidence for their interactions with other members of its community. Within acid mine drainage biofilms, apparently free-living ARMAN cells from a deeply branched archaeal lineage have volumes of 0.009–0.04 μm3 (mean ∼0.03±0.01 μm3), only ∼92 ribosomes, yet are frequent hosts for replicating viruses. Organization within the periplasm and partitioning of ribosomes to the inner surface of the cytoplasmic membrane may be factors in size minimization. Most cells contain enigmatic tubular structures of unknown function. The low ribosome copy number per unit volume, indicative of slow growth rates and targeting of cells by diverse viruses may account for the low abundance of ARMAN cells compared with other biofilm community members. Our results provide the first 3D analysis of structural features of these novel and enigmatic cells and their interactions with at least two types of viruses. Our findings also emphasize that new biological phenomena remain to be discovered among lower abundance organisms from novel uncultivated lineages.The ISME Journal (2009) 3, 159–167; doi:10.1038/ismej.2008.99; published online 23 October 2008 [ABSTRACT FROM AUTHOR]

Acid mine drainage (AMD) microbial communities contain microbial eukaryotes (both fungi and protists) that confer a biofilm structure and impact the abundance of bacteria and archaea and the community composition via grazing and other mechanisms. Since prokaryotes impact iron oxidation rates and thus regulate AMD generation rates, it is important to analyze the fungal and protistan populations. We utilized 18S rRNA and beta-tubulin gene phylogenies and fluorescent rRNA-specific probes to characterize the eukaryotic diversity and distribution in extremely acidic (pHs 0.8 to 1.38), warm (30 to 50°C), metal-rich (up to 269 mM Fe2+, 16.8 mM Zn, 8.5 mM As, and 4.1 mM Cu) AMD solutions from the Richmond Mine at Iron Mountain, Calif. A Rhodophyta (red algae) lineage and organisms from the Vahlkampfiidae family were identified. The fungal 18S rRNA and tubulin gene sequences formed two distinct phylogenetic groups associated with the classes Dothideomycetes and Eurotiomycetes. Three fungal isolates that were closely related to the Dothideomycetes clones were obtained. We suggest the name “Acidomyces richmondensis” for these isolates. Since these ascomycete fungi were morphologically indistinguishable, rRNA-specific oligonucleotide probes were designed to target the Dothideomycetes and Eurotiomycetes via fluorescent in situ hybridization (FISH). FISH analyses indicated that Eurotiomycetes are generally more abundant than Dothideomycetes in all of the seven locations studied within the Richmond Mine system. This is the first study to combine the culture-independent detection of fungi with in situ detection and a demonstration of activity in an acidic environment. The results expand our understanding of the subsurface AMD microbial community structure. [ABSTRACT FROM AUTHOR]

During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria. The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba. Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage samples, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage samples contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region VI of their 16S rRNA genes. The IVS does not match any sequence in current databases, but the predicted secondary structure forms well-defined stem loops. IVSs are uncommon in rRNA genes and appear to be confined to bacteria living in close association with eukaryotes. Based on the phylogenetic novelty of the endosymbiont sequences and initial culture-independent characterization, we propose the name "Candidatus Captivus acidiprotistae." To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat. [ABSTRACT FROM AUTHOR]

The dissolution of sulfide minerals such as pyrite (FeS2), arsenopyrite (FeAsS), chalcopyrite (CuFeS2), sphalerite (ZnS), and marcasite (FeS2) yields hot, sulfuric acid-rich solutions that contain high concentrations of toxic metals. In locations where access of oxidants to sulfide mineral surfaces is increased by mining, the resulting acid mine drainage (AMD) may contaminate surrounding ecosystems. Communities of autotrophic and heterotrophic archaea and bacteria catalyze iron and sulfur oxidation, thus may ultimately determine the rate of release of metals and sulfur to the environment. AMD communities contain fewer prokaryotic lineages than many other environments. However, it is notable that at least two archaeal and eight bacterial divisions have representatives able to thrive under the extreme conditions typical of AMD. AMD communities are characterized by a very limited number of distinct species, probably due to the small number of metabolically beneficial reactions available. The metabolisms that underpin these communities include organoheterotrophy and autotrophic iron and sulfur oxidation. Other metabolic activity is based on anaerobic sulfur oxidation and ferric iron reduction. Evidence for physiological synergy in iron, sulfur, and carbon flow in these communities is reviewed. The microbial and geochemical simplicity of these systems makes them ideal targets for quantitative, genomic-based analyses of microbial ecology and evolution and community function. [Copyright &y& Elsevier]

Summary We characterized the diversity of sulphate-reducing bacteria (SRB) associated with South African gold mine boreholes and deep aquifer systems in Washington State, USA. Sterile cartridges filled with crushed country rock were installed on two hydrologically isolated and chemically distinct sites at depths of 3.2 and 2.7 km below the land surface (kmbls) to allow development of biofilms. Enrichments of sulphate-reducing chemolithotrophic (H2 ) and organotrophic (lactate) bacteria were established from each site under both meso- and thermophilic conditions. Dissimilatory sulphite reductase (Dsr) and 16S ribosomal RNA (rRNA) genes amplified from DNA extracted from the cartridges were most closely related to the Gram-positive species Desulfotomaculum thermosapovorans and Desulfotomaculum geothermicum , or affiliated with a novel deeply branching clade. The dsr sequences recovered from the Washington State deep aquifer systems affiliated closely with the South African sequences, suggesting that Gram-positive sulphate-reducing bacteria are widely distributed in the deep subsurface. [ABSTRACT FROM AUTHOR]

Alkanes, single carbon methane to long‐chain hydrocarbons (e.g. hexadecane and tetradecane), are important carbon sources to anaerobic microbial communities. In anoxic environments, archaea are known to utilize and produce methane via the methyl‐coenzyme M reductase enzyme (MCR). Recent explorations of new environments, like deep sea sediments, that have coupled metagenomics and cultivation experiments revealed divergent MCRs, also referred to as alkyl‐coenzyme M reductases (ACRs) in archaea, with similar mechanisms as the C1 utilizing canonical MCR mechanism. These ACR enzymes have been shown to activate other alkanes such as ethane, propane and butane for subsequent degradation. The reversibility of canonical MCRs suggests that these non‐methane‐activating homologues (ACRs) might have similar reversibility, perhaps mediated by undiscovered lineages that produce alkanes under certain conditions. The discovery of these alternative alkane utilization pathways holds significant promise for a breadth of potential biotechnological applications in bioremediation, energy production and climate change mitigation. [ABSTRACT FROM AUTHOR]

Summary: Reduced substrates produced by the serpentinization reaction under hydration of olivine may have fuelled biological processes on early Earth. To understand the adaptive strategies and carbon metabolism of the microbes in the serpentinizing ecosystems, we reconstructed 18 draft genomes representing dominant species of Omnitrophicaeota, Gammaproteobacteria and Methanobacteria from the Manleluag serpentinizing spring in Zambales, Philippines (hyperalkaline and rich in methane and hydrogen). Phylogenomics revealed that two genomes were affiliated with a candidate phylum NPL‐UPA2 and the references of all our genomes were derived from ground waters, hot springs and the deep biosphere. C1 metabolism appears to be widespread as most of the genomes code for methanogenesis, CO oxidation and CO2 fixation. However, likely due to the low CO2 concentration and election acceptors, the biomass in the spring was extremely low (<103 cell/ml). Various Na+ and K+ transporters and Na+‐driving ATPases appear to be encoded by these genomes, suggesting that nutrient acquisition, bioenergetics and normal cytoplasmic pH were dependent on Na+ and K+ pumps. Our results advance our understanding of the metabolic potentials and bioenergetics of serpentinizing springs and provide a framework of the ecology of early Earth. [ABSTRACT FROM AUTHOR]

Words in polysynthetic languages, such as the Australian language Wubuy, can be semantically complex and translate into whole phrases in analytic languages such as English. This raises questions about whether such words are like words in English, or whether they are more like phrases. In the following, we examine Wubuy speakers' knowledge of word-internal morphological complexity in a word-preference task, in which we test the acceptability of complex words into which artificial pauses have been embedded at a range of morphological junctures. The results show that participants prefer unmodified words and words with pauses inserted at semantically transparent morphological junctures over words with pauses at other junctures. There is no preference for unmodified words over words with pauses at transparent junctures. These results suggest that speakers have access to some word-internal morphological information, and that complex words may share characteristics of both words and phrases in, for instance, English. [ABSTRACT FROM AUTHOR]

Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 165 ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer. [ABSTRACT FROM AUTHOR]

Most current models of nonnative speech perception (e.g., extended perceptual assimilation model, PAM-L2, Best & Tyler, 2007; speech learning model, Flege, 1995; native language magnet model, Kuhl, 1993) base their predictions on the native/nonnative status of individual phonetic/phonological segments. This paper demonstrates that the phonotactic properties of Japanese influence the perception of natively contrasting consonants and suggests that phonotactic influence must be formally incorporated in these models. We first propose that by extending the perceptual categories outlined in PAM-L2 to incorporate sequences of sounds, we can account for the effects of differences in native and nonnative phonotactics on nonnative and cross-language segmental perception. In addition, we test predictions based on such an extension in two perceptual experiments. In Experiment 1, Japanese listeners categorized and rated vowel–consonant–vowel strings in combinations that either obeyed or violated Japanese phonotactics. The participants categorized phonotactically illegal strings to the perceptually nearest (legal) categories. In Experiment 2, participants discriminated the same strings in AXB discrimination tests. Our results show that Japanese listeners are more accurate and have faster response times when discriminating between legal strings than between legal and illegal strings. These findings expose serious shortcomings in currently accepted nonnative perception models, which offer no framework for the influence of native language phonotactics. [ABSTRACT FROM AUTHOR]

• Nonnative (L2) vowel perception is affected by the phonotactic context. • Co-occurrence restriction and surface level alternation can affect how the same L2 vowel contrast is categorised, identified, and discriminated. • The same vowel contrast can have different perceptual patterns due to native phonological interference. • For L2-learning listeners, vowel perception in unfamiliar contexts is predictable from their linguistic experience, especially their vocabulary size in the target language. The study presented here examines how adult L2 listeners' L1 phonotactics interferes with L2 vowel perception in different consonantal contexts. We examined Mandarin listeners' perception of the English /ei/-/iː/ vowel contrast in three onset consonantal contexts, /p f w/, which represent different phonotactic scenarios with respect to the permissibility of Mandarin phonology. L1 Mandarin listeners (N = 42) completed a series of three tasks: a categorisation task, a vowel identification task, and an AXB discrimination task. The results show that English /ei/-/iː/ are perceived as highly contrastive in the /p/ context because both /pei/ and /piː/ constitute a licit sequence in Mandarin phonology. However, participants experience substantial /ei/-/iː/ category confusion in the /f/ and /w/ contexts, where Mandarin listeners repair perceptually by modifying the vowel quality in illicit (unattested) consonant–vowel sequences, i.e., */fiː/ → /fei/ and */wiː/ → /wei/. Further exploratory analyses indicate that L2 listeners' vowel perception in unfamiliar phonotactic contexts is associated with their target language experience, typically indicated by their L2 vocabulary size. The findings thus suggest that the acquisition of novel phonotactic regularities is tied to increased experience with the L2 lexicon. [ABSTRACT FROM AUTHOR]

The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere. [ABSTRACT FROM AUTHOR]

Substantial research has established that place of articulation of stop consonants (labial, alveolar, velar) are reliably differentiated using a number of acoustic measures such as closure duration, voice onset time (VOT), and spectral measures such as centre of gravity and the relative energy distribution in the mid-to-high spectral range of the burst. It is unclear, however, whether such measurable acoustic differences are present in multiple place of articulation contrasts among coronal stops. This article presents evidence from the highly endangered indigenous Australian language Wubuy, which maintains a 4-way coronal stop place contrast series in all word positions. The authors examine the temporal and burst characteristics of /t9 t / in three prosodic positions (utterance-initial, word-initial but phrase medial, and word-medial). The results indicate that VOT, closure duration, and the spectral quality of the burst may indeed differentiate multiple coronal place contrasts, in most positions, although measures that distinguish the apical contrast in absolute initial position remain elusive. The authors also examine measures (spectrum kurtosis, spectral tilt) previously used in other studies of multiple coronals in Australian languages. These results suggest that the authors' measures perform at least as well as those previously applied to multiple coronals in other Australian languages. [ABSTRACT FROM AUTHOR]

Particulate membrane-associated hydrocarbon monooxygenases ( pHMOs) are critical components of the aerobic degradation pathway for low molecular weight hydrocarbons, including the potent greenhouse gas methane. Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon-rich hydrothermal plumes in the Guaymas Basin ( GB) and nearby background waters in the deep Gulf of California. Seven distinct phylogenetic groups of pHMO were present and transcriptionally active in both plume and background waters, including several that are undetectable with currently available polymerase chain reaction ( PCR) primers. The seven groups of pHMOs included those related to a putative ethane oxidizing Methylococcaceae-like group, a group of the SAR324 Deltaproteobacteria, three deep-sea clades (Deep sea-1/symbiont-like, Deep sea-2/ PS-80 and Deep sea-3/ OPU3) within gammaproteobacterial methanotrophs, one clade related to Group Z and one unknown group. Differential abundance of pHMO gene transcripts in plume and background suggests niche differentiation between groups. Corresponding 16 S rRNA genes reflected similar phylogenetic and transcriptomic abundance trends. The novelty of transcriptionally active pHMOs we recovered from a hydrocarbon-rich hydrothermal plume suggests there are significant gaps in our knowledge of the diversity and function of these enzymes in the environment. [ABSTRACT FROM AUTHOR]

Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a member of Leptospirillum group III, a lineage in the Nitrospirae phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm sample naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of ∼106 cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of Leptospirillum group III and that the culture is axenic. We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms. [ABSTRACT FROM AUTHOR]

Studies the distribution of microbial small-subunit (SSU) ribosomal (r)RNA in relation to chemical profiles using molecular biological methods. Relationship between ribosome content, growth rate and starvation; Comparison between sediment and water column rRNA concentrations; Role of grazers in seasonal changes in SSU rRNA and nitrate concentration.

Examines the microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the open waters of Lake Michigan. Significance of atmospheric N[sub 2] on the lake; Role of bacteria in the nitrogen fixation; Extent of nitrogen fixation competence during stratified season.

Summary: Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single‐gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher‐resolution frameworks are needed to resolve the physiological interactions within these algal–bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae‐associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae‐associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria. [ABSTRACT FROM AUTHOR]

Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily low rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River Estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmax expressed on a per-cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (D-phenylalanine and L-ornithine) increased relative to enzymes that act on L-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded-DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes. [ABSTRACT FROM AUTHOR]

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e. members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e. parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph -lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently. [ABSTRACT FROM AUTHOR]

The functional role of membrane-bound carbonic anhydrases (CAs) has been of keen interest in the past decade, and in particular, studies have linked CA in red muscle, heart, and eye to enhanced tissue oxygen extraction in bony fishes (teleosts). However, the number of purported membrane-bound CA isoforms in teleosts, combined with the imperfect system of CA isoform nomenclature, present roadblocks for ascribing physiological functions to particular CA isoforms across different teleost lineages. Here we developed an organizational framework for membrane-bound CAs in teleosts, providing the latest phylogenetic analysis of extant CA4 and CA4-like isoforms. Our data confirm that there are three distinct isoforms of CA4 (a, b, and c) that are conserved across major teleost lineages, with the exception of CA4c gene being lost in salmonids. Tissue distribution analyses suggest CA4a functions in oxygen delivery across teleost lineages, while CA4b may be specialized for renal acid-base balance and ion regulation. This work provides an important foundation for researchers to elucidate the functional significance of CA4 isoforms in fishes. [Display omitted] • Phylogeny confirms three distinct isoforms of fish carbonic anhydrase 4 (CA4). • CA4a may be the isoform of interest for enhanced tissue oxygen delivery studies. • In salmonids CA4b may be specialized for renal acid-base balance and ion regulation. • CA4c is lost in salmonids and its physiological role is unclear. [ABSTRACT FROM AUTHOR]

The article discusses horizontal gene transfer between the extremophilic red alga Galdieria sulphuraria and prokaryotes. Topics include sequencing of G. sulphuraria's 13.7-megabase genome to elucidate the underlying molecular mechanisms of adaptation to its environment, the metabolic flexibility of G. sulphuraria, which was able to grow either photoautotrophically or heterotrophically on more than 50 carbon sources, the facilitation of environmental adaptation by horizontal gene transfer from various bacteria and archaea, which the authors note is often followed by gene family expansion, and the percentage of protein-coding genes of G. sulphuraria acquired horizontally and their role in several ecological processes, such as glycerol uptake and metabolism.

Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context we investigated links between genotype and ecology of two genotypic groups of Leptospirillum group II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 165 rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature. consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry-based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the ∼15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies. [ABSTRACT FROM AUTHOR]

We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage bioflim. Community proteomic analysis of the genomically characterized sample and two other biofllms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofllms. Interestingly, Leptospirillum group II uses a methyldependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III. [ABSTRACT FROM AUTHOR]

Alkaline, sulfidic, 54 to 60°C, 4 to 53 million-year-old meteoric water emanating from a borehole intersecting quartzite-hosted fractures >3.3 km beneath the surface supported a microbial community dominated by a bacterial species affiliated with Desulfotomaculum spp. and an archaeal species related to Methanobacterium spp. The geochemical homogeneity over the 659-m length of the borehole, the lack of dividing cells, and the absence of these microorganisms in mine service water support an indigenous origin for the microbial community. The coexistence of these two microorganisms is consistent with a limiting flux of inorganic carbon and SO42- in the presence of high pH, high concentrations of H2 and CH4, and minimal free energy for autotrophic methanogenesis. Sulfide isotopic compositions were highly enriched, consistent with microbial SO42- reduction under hydrologic isolation. An analogous microbial couple and similar abiogenic gas chemistry have been reported recently for hydrothermal carbonate vents of the Lost City near the Mid-Atlantic Ridge (D. S. Kelly et al., Science 307:1428-1434, 2005), suggesting that these features may be common to deep subsurface habitats (continental and marine) bearing this geochemical signature. The geochemical setting and microbial communities described here are notably different from microbial ecosystems reported for shallower continental subsurface environments. [ABSTRACT FROM AUTHOR]

Using genomic and mass spectrometry-based proteomic methods, weevaluated gene expression, identified key activities, and examinedpartitioning of metabolic functions in a natural acid mine drainage(AMD) microbial biofilm community. We detected 2033 proteins from thefive most abundant species in the biofilm, including 48% of thepredicted proteins from the dominant biofilm organism, Leptospirillumgroup II. Proteins involved in protein refolding and response tooxidative stress appeared to be highly expressed, which suggests thatdamage to biomolecules is a key challenge for survival. We validated andestimated the relative abundance and cellular localization of 357 uniqueand 215 conserved novel proteins and determined that one abundant novelprotein is a cytochrome central to iron oxidation and AMD formation. [ABSTRACT FROM AUTHOR]