Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T))

Natural Biodegradation of Vinyl Chloride and cis-Dichloroethene in Aerobic and Suboxic Conditions

Chlorinated ethene (CE) groundwater contamination is commonly treated through anaerobic biodegradation (i.e., reductive dechlorination) either as part of an engineered system or through natural attenuation. Aerobic biodegradation has also been recognized as a potentially significant pathway for the removal of the lower CEs cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC). However, the role of aerobic biodegradation under low oxygen conditions typical of contaminated groundwater is unclear. Bacteria capable of aerobic VC biodegradation appear to be common in the environment, while aerobic biodegradation of cDCE is less common and little is known regarding the organisms responsible. In this study, we investigate the role of aerobic cDCE and VC biodegradation in a mixed contaminant plume (including CEs, BTEX, and ketones) at Naval Air Station North Island, Installation Restoration Site 9. Sediment and groundwater collected from the plume source area, mid-plume, and shoreline were used to prepare microcosms under fully aerobic (8 mg/L dissolved oxygen (DO)) and suboxic (< 1 mg/L DO) conditions. In the shoreline microcosms, VC and cDCE were rapidly degraded under suboxic conditions (100% and 77% removal in < 62 days). In the suboxic VC microcosms, biodegradation was associated with a > 5 order of magnitude increase in the abundance of functional gene etnE, part of the aerobic VC utilization pathway. VC and cDCE were degraded more slowly under fully aerobic conditions (74% and 30% removal) in 110 days. High-throughput 16S rRNA and etnE sequencing suggest the presence of novel VC- and cDCE-degrading bacteria. These results suggest that natural aerobic biodegradation of cDCE and VC is occurring at the site and provide new evidence that low (< 1 mg/L) DO levels play a significant role in natural attenuation of cDCE and VC.

Large publishing consortia produce higher citation impact research but coauthor contributions are hard to evaluate

This paper introduces a simple agglomerative clustering method to identify large publishing consortia with at least 20 authors and 80% shared authorship between articles. Based on Scopus journal articles from 1996–2018, under these criteria, nearly all (88%) of the large consortia published research with citation impact above the world average, with the exceptions being mainly the newer consortia, for which average citation counts are unreliable. On average, consortium research had almost double (1.95) the world average citation impact on the log scale used (Mean Normalised Log Citation Score). At least partial alphabetical author ordering was the norm in most consortia. The 250 largest consortia were for nuclear physics and astronomy, involving expensive equipment, and for predominantly health-related issues in genomics, medicine, public health, microbiology and neuropsychology. For the health-related issues, except for the first and last few authors, authorship seem to primarily indicate contributions to the shared project infrastructure necessary to gather the raw data. It is impossible for research evaluators to identify the contributions of individual authors in the huge alphabetical consortia of physics and astronomy and problematic for the middle and end authors of health-related consortia. For small-scale evaluations, authorship contribution statements could be used when available.

The water depth-dependent co-occurrence patterns of marine bacteria in shallow and dynamic Southern Coast, Korea

To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.

Genome-Based Taxonomic Classification of Bacteroidetes

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris

Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5–6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae—all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET substrate. Future research is required to investigate microscale functional interactions at the plastic surface.

An Unusual Inverted Saline Microbial Mat Community in an Interdune Sabkha in the Rub' al Khali (the Empty Quarter), United Arab Emirates

Salt flats (sabkha) are a recognized habitat for microbial life in desert environments and as analogs of habitats for possible life on Mars. Here we report on the physical setting and microbiology of interdune sabkhas among the large dunes in the Rub' al Khali (the Empty Quarter) in Liwa Oasis, United Arab Emirates. The salt flats, composed of gypsum and halite, are moistened by relatively fresh ground water. The result is a salinity gradient that is inverted compared to most salt flat communities with the hypersaline layer at the top and freshwater layers below. We describe and characterize a rich photosynthetically-based microbial ecosystem that is protected from the arid outside environment by a translucent salt crust. Gases collected from sediments under shallow ponds in the sabkha contain methane in concentrations as high as 3400 ppm. The salt crust could preserve biomarkers and other evidence for life in the salt after it dries out. Chloride-filled depressions have been identified on Mars and although surface flow of water is unlikely on Mars today, ground water is possible. Such a near surface system with modern groundwater flowing under ancient salt deposits could be present on Mars and could be accessed by surface rovers.

Spatial-temporal variations and diversity of the bacterioplankton communities in the coastal waters of Kuwait

The dynamics and composition of the bacterial community in the coastal waters of Kuwait are poorly understood. In this study, the spatial-temporal variations in the bacterial composition in the surface water along the Kuwaiti coast was examined by 16S rRNA denaturing gradient gel electrophoresis (DGGE) fingerprinting and phylogeny analyses. The sampling sites were Kuwait Bay, Al-Sabbiya (north of the bay) and Al-Khairan (to the south). The bacterial composition was more variable in the summer for all sites. A cluster analysis of the DGGE fingerprint revealed two main clusters, indicating a temporal similarity between sites. Kuwait Bay and Al-Khairan were more similar to each other than to Al-Sabbiya. The bacterial community composition exhibited distinctive spatial variations, with more diversity at Al-Khairan and less diversity at Al-Sabbiya. At all sites, the dominant bacteria were Alphaproteobacteria, in particular Rhodobacteraceae, followed by Alteromonadaceae (Gammaproteobacteria) and Bacteroidetes.

Global identification of O-GlcNAc transferase (OGT) interactors by a human proteome microarray and the construction of an OGT interactome

O-Linked β-N-acetylglucosamine (O-GlcNAcylation) is an important protein PTM, which is very abundant in mammalian cells. O-GlcNAcylation is catalyzed by O-GlcNAc transferase (OGT), whose substrate specificity is believed to be regulated through interactions with other proteins. There are a handful of known human OGT interactors, which is far from enough for fully elucidating the substrate specificity of OGT. To address this challenge, we used a human proteome microarray containing ~17,000 affinity-purified human proteins to globally identify OGT interactors and identified 25 OGT-binding proteins. Bioinformatics analysis showed that these interacting proteins play a variety of roles in a wide range of cellular functions and are highly enriched in intra-Golgi vesicle-mediated transport and vitamin biosynthetic processes. Combining newly identified OGT interactors with the interactors identified prior to this study, we have constructed the first OGT interactome. Bioinformatics analysis suggests that the OGT interactome plays important roles in protein transportation/localization and transcriptional regulation. The novel OGT interactors that we identified in this study could serve as a starting point for further functional analysis. Because of its high-throughput and parallel analysis capability, we strongly believe that protein microarrays could be easily applied for the global identification of regulators for other key enzymes.

Luteibaculum oceani gen. nov., sp. nov., a carotenoid-producing, lipolytic bacterium isolated from surface seawater, and emended description of the genus Owenweeksia Lau et al. 2005

A yellow-pigmented, Gram-staining-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming, lipolytic and gliding marine bacterium designated strain CC-AMWY-103B(T) was isolated from surface seawater collected at Kending, Taiwan. The strain shared the highest 16S rRNA gene sequence similarity of 89.4% with Owenweeksia hongkongensis JCM 12287(T) and Brumimicrobium mesophilum YH207(T), and established a distinct phyletic lineage associated with the members of the family Cryomorphaceae. The polar lipid profile of strain CC-AMWY-103B(T) consisted of phosphatidylethanolamine, ten unidentified lipids and four unidentified aminolipids. The major fatty acids (>5% of the total) were iso-C15 : 0, iso-C15 : 1 G, C15 : 1ω5c, iso-C17 : 0 3-OH and C15 : 1ω8c. The DNA G+C content was 44.2 ± 0.3 mol%. The predominant respiratory quinone was menaquinone-6 (MK-6) and the major polyamine was spermidine. Based on its genetic, phylogenetic, phenotypic and chemotaxonomic distinctiveness, strain CC-AMWY-103B(T) is proposed to represent a distinct member of the family Cryomorphaceae, for which the name Luteibaculum oceani gen. nov., sp. nov. is proposed; the type strain of Luteibaculum oceani is CC-AMWY-103B(T) ( = JCM 18817(T) = BCRC 80551(T)). An emended description of the genus Owenweeksia is also proposed.