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Aquaporins are integral membrane proteins that facilitate the diffusion of water and other small, uncharged solutes across the cellular membrane and are widely distributed in organisms from humans to bacteria. However, the characteristics of prokaryotic aquaporins remain largely unknown. We investigated the distribution and sequence characterization of aquaporins in prokaryotic organisms and summarized the transport characteristics, physiological functions, and regulatory mechanisms of prokaryotic aquaporins. Aquaporin homologues were identified in 3315 prokaryotic genomes retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, but the protein clustering pattern is not completely congruent with the phylogeny of the species that carry them. Moreover, prokaryotic aquaporins display diversified aromatic/arginine constriction region (ar/R) amino acid compositions, implying multiple functions. The typical water and glycerol transport characterization, physiological functions, and regulations have been extensively studied in Escherichia coli AqpZ and GlpF. A Streptococcus aquaporin has recently been verified to facilitate the efflux of endogenous H2O2, which not only contributes to detoxification but also to species competitiveness, improving our understanding of prokaryotic aquaporins. Furthermore, recent studies revealed novel regulatory mechanisms of prokaryotic aquaporins at post-translational level. Thus, we propose that intensive investigation on prokaryotic aquaporins would extend the functional categories and working mechanisms of these ubiquitous, intrinsic membrane proteins.

Background: Microorganisms are widespread in all environments, including in and on animal bodies. The gut microbiome has an essential influence on fish health, and is affected by several persistent and harmful organic and inorganic contaminants. Considering the shifts in gut microbiota composition observed in those studies, we hypothesized that certain microbial groups in the gut can serve as indicators of pollution. To test this hypothesis, we explored the possibility of identifying key microbial players that indicate environmental contamination. Methods: Published 16S rRNA gene amplicon sequencing data generated from the gut microbiota of Atlantic cod caught in geographically different Norwegian waters were used for bacterial diversity comparison. Results: Different microbiomes were identified between the northern Norway and southern Norway samples. Several bacterial genera previously identified as polycyclic aromatic hydrocarbon degraders were present only in the samples collected in the southern Norway area, suggesting fish contamination with oil-related compounds. Conclusions: The results contribute to the identification of bacterial taxa present in the Atlantic cod gut that indicate fish exposure to contaminants in the marine environment.

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Recently, there has been an increase in the number of whole bacterial genomes sequenced, mainly due to the advancing of next-generation sequencing technologies. In face of this, there is a need to provide new analytical alternatives that can follow this advance. Given our current knowledge about the genomic plasticity of bacteria and that those genomic regions can uncover important features about this microorganism, our goal was to develop a fast methodology based on maximum entropy (ME) to guide the researcher to regions that could be prioritized during the analysis. This methodology was compared with other available methods. In addition, ME was applied to eight different bacterial genera. The methodology consists of two main steps: processing the nucleotide sequence and ME calculation. We applied ME to Xanthomonas axonopodis pv. citri 306 (XAC) and Xanthomonas campestris pv. campestris ATCC 33913 (XCC), both of which have their anomalous regions well documented. We then compared our results against those from Alien Hunter, HGT-DB, Islander, IslandPath, and SIGI-HMM. ME was shown to be superior in terms of efficiency and analysis duration. Besides, ME only needs the genome sequence in FASTA format as input. The proposed strategy based on ME is able to help in bacterial genome exploration. This is a simple and fast strategy for individual genomes in comparison with other available methods, without relying on previous annotation and alignments. This methodology can also be a new option in the early stages of analysis of newly sequenced bacterial genomes. [ABSTRACT FROM AUTHOR]

Biological treatment represents a key step in nutrient removal from wastewater. Until now these process has mainly been considered prokaryotic, with the interactions between prokaryotes and eukaryotes not being properly explored. We therefore investigated the co-occurrence of eukaryotes and prokaryotes in biological nitrogen removal biofilms. We found that biofilms in the nitrifying reactor contained the highest diversity and abundance of both prokaryotes and eukaryotes, with nearly three times higher prokaryote species richness than for the denitrifying reactor. The positive associations between eukaryote abundance and prokaryote diversity could potentially be explained by mutualism - and/or predator/prey interactions. Further mechanistic insight, however, is needed to determine the main diversifying mechanisms. In summary, eukaryote and prokaryote interactions seem to play a fundamental yet underexplored role in biological wastewater treatment. Significance and Impact of the Study Eukaryote and prokaryote interactions may play an important role in wastewater treatment. This study found that prokaryote species richness was nearly three times higher in the aerobe nitrification than in an anaerobe denitrification reactor, coinciding with the highest level of eukaryotes. This knowledge can be important in process control, and potentially in the development of novel approaches based on nitrate accumulating denitrifying eukaryotes. [ABSTRACT FROM AUTHOR]

ABSTRACT The discovery of the numerical importance of viruses in a variety of (aquatic) ecosystems has changed our perception of their importance in microbial processes. Bacteria and Archaea undoubtedly represent the most abundant cellular life forms on Earth and past estimates of viral numbers (represented mainly by viruses infecting prokaryotes) have indicated abundances at least one order of magnitude higher than that of their cellular hosts. Such dominance has been reflected most often by the virus-to-prokaryote ratio ( VPR), proposed as a proxy for the relationship between viral and prokaryotic communities. VPR values have been discussed in the literature to express viral numerical dominance (or absence of it) over their cellular hosts, but the ecological meaning and interpretation of this ratio has remained somewhat nebulous or contradictory. We gathered data from 210 publications (and additional unpublished data) on viral ecology with the aim of exploring VPR. The results are presented in three parts: the first consists of an overview of the minimal, maximal and calculated average VPR values in an extensive variety of different environments. Results indicate that VPR values fluctuate over six orders of magnitude, with variations observed within each ecosystem. The second part investigates the relationship between VPR and other indices, in order to assess whether VPR can provide insights into virus-host relationships. A positive relationship was found between VPR and viral abundance ( VA), frequency of visibly infected cells ( FVIC), burst size ( BS), frequency of lysogenic cells ( FLC) and chlorophyll a ( Chl a) concentration. An inverse relationship was detected between VPR and prokaryotic abundance ( PA) (in sediments), prokaryotic production ( PP) and virus-host contact rates ( VCR) as well as salinity and temperature. No significant relationship was found between VPR and viral production ( VP), fraction of mortality from viral lysis ( FMVL), viral decay rate ( VDR), viral turnover ( VT) or depth. Finally, we summarize our results by proposing two scenarios in two contrasting environments, based on current theories on viral ecology as well as the present results. We conclude that since VPR fluctuates in every habitat for different reasons, as it is linked to a multitude of factors related to virus-host dynamics, extreme caution should be used when inferring relationships between viruses and their hosts. Furthermore, we posit that the VPR is only useful in specific, controlled conditions, e.g. for the monitoring of fluctuations in viral and host abundance over time. [ABSTRACT FROM AUTHOR]

Background: Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects. Results: We utilized a deeply-sampled dataset of MS/MS proteomic analysis covering 9 timepoints spanning the Escherichia coli growth cycle and an unbiased PTM search strategy to construct a temporal map of abundance for all PTMs within a 400 Da window of mass shifts. Using this map, we are able to identify novel targets and temporal patterns for N-terminal Nα acetylation, C-terminal glutamylation, and asparagine deamidation. Furthermore, we identify a possible relationship between N-terminal Nα acetylation and regulation of protein degradation in stationary phase, pointing to a previously unrecognized biological function for this poorly-understood PTM. Conclusions: Unbiased detection of PTM in MS/MS proteomics data facilitates the discovery of novel modification types and previously unobserved dynamic changes in modification across growth timepoints. [ABSTRACT FROM AUTHOR]

Asian dust events transport the airborne bacteria in Chinese desert regions as well as mineral particles and influence downwind area varying biological ecosystems and climate changes. However, the airborne bacterial dynamics were rarely investigated in the Gobi desert area, where dust events are highly frequent. In this study, air samplings were sequentially performed at a 2-m high above the ground at the sampling site located in desert area (Tsogt-Ovoo of Gobi desert; Mongolia 44.2304°N, 105.1700°E). During the dust event days, the bacterial cells and mineral particles increased to more than tenfold of concentrations. MiSeq sequencing targeting 16S ribosomal DNA revealed that the airborne bacteria in desert area mainly belonged to the classes Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Bacilli, Alpha-proteobacteria, Beta-proteobacteria, and Gamma-proteobacteria. The bacterial community structures were different between dust events and non-dust events. The air samples collected at the dust events indicated high abundance rates of Alpha-proteobacteria, which were reported to dominate on the leaf surfaces of plants or in the saline lake environments. After the dust events, the members of Firmicutes ( Bacilli) and Bacteroidetes, which are known to form endospore and attach with coarse particles, respectively, increased their relative abundances in the air samples. Presumably, the bacterial compositions and diversities in atmosphere significantly vary during dust events, which carry some particles from grassland (phyllo-sphere), dry lake, and sand surfaces, as well as some bacterial populations such as Firmicutes and Bacteroidetes maintain in the atmosphere for longer time. [ABSTRACT FROM AUTHOR]

A comparative study for abundance, biomass and diversity was carried out for the prokaryote, meiofauna and macrofauna communities at three depth stations (1200, 1800 and 2100 m) along the Malta Escarpment (Mediterranean Sea). Our investigation showed a two-fold increase with depth in prokaryote abundance; the contribution of prokaryote biomass to the total benthic biomass was predominant at all depths. Bacteria were the dominant prokaryote component and Archaea formed a considerable fraction (20%-30%) of the prokaryote assemblages. The meio- and macrofauna abundances and meiofauna biomass did not decrease significantly with depth but macrofauna biomass did. The α diversity did not follow a clear bathymetric trend for both nematode and macrofauna species. Probably because of the large number of eurybathic nematode genera, nor did the turnover diversity in nematode composition change down the depth gradient. Conversely, for the macrofauna there was a perceptible change in community composition between the shallowest station and the two deeper stations. Food availability affected only the macrobenthic component. The increase in the prokaryote organisms with depth and the dominance of nematodes and macrofauna deposit feeders suggest active grazing by the two benthic components on microbes. This would transfer energy to the higher trophic levels through the microbial compartment.

The degradation of messenger RNA is of universal importance for controlling gene expression. It directly affects protein synthesis by modulating the amount of mRNA available for translation. Regulation of mRNA decay provides an efficient means to produce just the proteins needed and to rapidly alter patterns of protein synthesis. In bacteria, the half-lives of individual mRNAs can differ by as much as two orders of magnitude, ranging from seconds to an hour. Most of what we know today about the diverse mechanisms of mRNA decay and maturation in prokaryotes comes from studies of the two model organisms Escherichia coli and Bacillus subtilis. Their evolutionary distance provided a large picture of potential pathways and enzymes involved in mRNA turnover. Among them are three ribonucleases, two of which have been discovered only recently, which have a truly general role in the initiating events of mRNA degradation: RNase E, RNase J and RNase Y. Their enzymatic characteristics probably determine the strategies of mRNA metabolism in the organism in which they are present. These ribonucleases are coded, alone or in various combinations, in all prokaryotic genomes, thus reflecting how mRNA turnover has been adapted to different ecological niches throughout evolution.

• Combined multiple proxies are used to identify cyanobacteria-dominant kerogen. • Kerogen is dominated by cyanobacteria in Proterozoic before the rise of algae. • Phanerozoic cyanobacteria-dominant kerogen is formed in ocean anoxic conditions. • Macromolecules from cyanobacteria cell walls could be directly preserved as kerogen. • Degradable molecules probably form kerogen through the degradation-recondensation pathway. Cyanobacteria have evolved since the early history of the Earth and played a critical role in Earth's carbon cycle. However, the contribution of cyanobacteria to organic carbon burial has rarely been underscored due to their lack of lipids membrane, which are refractory materials ready for preservation in sediments. To clarify the role of cyanobacteria in organic carbon burial, we focus on kerogen, which is the precursor of petroleum and also one of the most important organic carbon pools. We first review the physiological and environmental characteristics of modern cyanobacteria, which sets the theoretical foundations for kerogen formation. Cyanobacteria cell wall contains refractory algaenan, biomacromolecules rich in long-chain aliphatic structures, which are ready to be preserved in sediments and generate hydrocarbons during pyrolysis. Cyanobacteria can also form dense blooms in special environments, such as high temperatures with limited nitrogen supply. We then compile the cyanobacteria-dominant kerogen to reveal its temporal distribution in geological history. The cyanobacteria-dominant kerogen is identified mainly by three criteria including high total organic carbon, high hopane/sterane ratio, and high 2-MeHop index. The results show that the biological parent material of Proterozoic kerogen is dominated by cyanobacteria when eukaryotic algae did not experience massive blooms. In Phanerozoic, cyanobacteria-dominant kerogen is formed in episodic ocean anoxic conditions, where strong denitrification reduced nitrogen supply and hindered the growth of eukaryotic algae. Rock-Eval results show that cyanobacteria-dominant kerogen could have higher hydrogen content than cyanobacteria algaenan. In addition, we compare two Proterozoic cyanobacteria-dominant black shales deposited in anoxic and partially oxic environments and find that the kerogen formed in the anoxic environment has much higher hydrocarbon potential than that formed in the oxic environment. The difference in hydrocarbon potential, together with kerogen compositions, indicates that decomposable molecules with higher hydrocarbon potential could also form kerogen besides refractory algaenan. Based on this holistic review, we propose a model for cyanobacteria flourishing and organic matter preservation and highlight the critical role cyanobacteria played in organic carbon burial in Earth's history. [ABSTRACT FROM AUTHOR]

The complete genome sequence of strain NIBR10 was sequenced using PacBio RS II (Pacific Biosciences) sequencing platform. The 4,006,378-bp genome has a G + C content of 66.89% and around 3,832 coding sequences. Genomic data will provide valuable research for natural taxonomy and comparative genomics of the genus Brevundimonas ., Competing Interests: The authors declare no conflict of interest.

The increasing size of timetrees in recent years has led to a focus on diversification analyses to better understand patterns of macroevolution. Thus far, nearly all studies have been conducted with eukaryotes primarily because phylogenies have been more difficult to reconstruct and calibrate to geologic time in prokaryotes. Here, we have estimated a timetree of 11,784 'species' of prokaryotes and explored their pattern of diversification. We used data from the small subunit ribosomal RNA along with an evolutionary framework from previous multi-gene studies to produce three alternative timetrees. For each timetree we surprisingly found a constant net diversification rate derived from an exponential increase of lineages and showing no evidence of saturation (rate decline), the same pattern found previously in eukaryotes. The implication is that prokaryote diversification as a whole is the result of the random splitting of lineages and is neither limited by existing diversity (filled niches) nor responsive in any major way to environmental changes. [ABSTRACT FROM AUTHOR]

Current evolutionary models suggest that Eukaryotes originated from within Archaea instead of being a sister lineage. To test this model of ancient evolution, we review recent studies and compare the three major information processing subsystems of replication, transcription and translation in the Archaea and Eukaryotes. Our hypothesis is that if the Eukaryotes arose within the archaeal radiation, their information processing systems will appear to be one of kind and not wholly original. Within the Eukaryotes, the mammalian or human systems are emphasized because of their importance in understanding health. Biochemical as well as genetic studies provide strong evidence for the functional similarity of archaeal homologs to the mammalian information processing system and their dissimilarity to the bacterial systems. In many independent instances, a simple archaeal system is functionally equivalent to more elaborate eukaryotic homologs, suggesting that evolution of complexity is likely an central feature of the eukaryotic information processing system. Because fewer components are often involved, biochemical characterizations of the archaeal systems are often easier to interpret. Similarly, the archaeal cell provides a genetically and metabolically simpler background, enabling convenient studies on the complex information processing system. Therefore, Archaea could serve as a parsimonious and tractable host for studying human diseases that arise in the information processing systems. [ABSTRACT FROM AUTHOR]

Background: The navigation of magnetotactic bacteria relies on specific intracellular organelles, the magnetosomes, which are membrane-enclosed crystals of magnetite aligned into a linear chain. The magnetosome chain acts as a cellular compass, aligning the cells in the geomagnetic field in order to search for suitable environmental conditions in chemically stratified water columns and sediments. During cytokinesis, magnetosome chains have to be properly positioned, cleaved and separated in order to be evenly passed into daughter cells. In Magnetospirillum gryphiswaldense, the assembly of the magnetosome chain is controlled by the actin-like MamK, which polymerizes into cytoskeletal filaments that are connected to magnetosomes through the acidic MamJ protein. MamK filaments were speculated to recruit the magnetosome chain to cellular division sites, thus ensuring equal organelle inheritance. However, the underlying mechanism of magnetic organelle segregation has remained largely unknown. Results: Here, we performed in vivo time-lapse fluorescence imaging to directly track the intracellular movement and dynamics of magnetosome chains as well as photokinetic and ultrastructural analyses of the actin-like cytoskeletal MamK filament. We show that magnetosome chains undergo rapid intracellular repositioning from the new poles towards midcell into the newborn daughter cells, and the driving force for magnetosomes movement is likely provided by the pole-to-midcell treadmilling growth of MamK filaments. We further discovered that splitting and equipartitioning of magnetosome chains occurs with unexpectedly high accuracy, which depends directly on the dynamics of MamK filaments. Conclusion: We propose a novel mechanism for prokaryotic organelle segregation that, similar to the type-II bacterial partitioning system of plasmids, relies on the action of cytomotive actin-like filaments together with specific connectors, which transport the magnetosome cargo in a fashion reminiscent of eukaryotic actin-organelle transport and segregation mechanisms. [ABSTRACT FROM AUTHOR]

Members of the TrmB family act as global transcriptional regulators for the activation or repression of sugar ABC transporters and central sugar metabolic pathways, including glycolytic, gluconeogenic, and other metabolic pathways, and also as chromosomal stabilizers in archaea. As a relatively newly classified transcriptional regulator family, there is limited experimental evidence for their role in Thermococcales, halophilic archaeon Halobacterium salinarum NRC1, and crenarchaea Sulfolobus strains, despite being one of the extending protein families in archaea. Recently, the protein structures of Pyrococcus furiosus TrmB and TrmBL2 were solved, and the transcriptomic data uncovered by microarray and ChIP-Seq were published. In the present review, recent evidence of the functional roles of TrmB family members in archaea is explained and extended to bacteria. [ABSTRACT FROM AUTHOR]

The Mesoproterozoic Hongshuizhuang Formation (∼1.4 Ga) from northern China consists of organic-rich sediments which record important environmental and biological information from that time. Organic and element geochemistry techniques were used to assess the syngeneity and indigeneity of hydrocarbons, and the thermal maturity and biological sources of the organic matter in the Hongshuizhuang Formation. Results from a slice-extraction experiment indicate that the exterior of the core was subjected to contamination from drilling, sampling and storage, whereas the organic matter in the interior shale core slices was indigenous. The organic matter in the interior argillaceous dolomite core slices might have been affected by the migration of oil. It is important to remove the outside of the core prior to solvent extraction, as this increases the possibility of analysis of indigenous hydrocarbons. The source rocks of the oil are the black shales of the Hongshuizhuang Formation. Aliphatic and aromatic hydrocarbon distributions indicate that the Hongshuizhuang Formation samples have a low thermal maturity in the early to middle oil window (0.6–0.8 %Ro equivalent), based on comparison with middle Velkerri Formation rocks of about the same age in the McArthur Basin, northern Australia. These data are consistent with results based on the values of T max and protobitumen reflectance, and suggest that the samples contain well preserved organic matter that has not been thermally destroyed. The redox conditions indicated by the pristane/phytane (Pr/Ph) ratios are not consistent with other evidence. The correlations between n -C 20− / n -C 21+ , major elements and Pr/Ph indicate that the Pr/Ph ratios are influenced by biological sources and mineralogy, rather than by redox conditions. Pr and Ph may have been derived not only from chlorophyll-a, but also from archaea. The short and long chain n -alkanes in the Hongshuizhuang Formation were derived from anoxic clay-rich environments and oxic carbonate-rich environments, respectively. The biomarkers observed in the Hongshuizhuang Formation indicate that the organic matter was primarily derived from prokaryotes. [ABSTRACT FROM AUTHOR]

CRISPR-Cas are self-/nonself-discriminating systems found in prokaryotic cells. They represent a remarkable example of molecular memory that is hereditarily transmitted. Their discovery can be considered as one of the first fruits of the systematic exploration of prokaryotic genomes. Although this genomic feature was serendipitously discovered in molecular biology studies, it was the availability of multiple complete genomes that shed light about their role as a genetic immune system. Here we tell the story of how this discovery originated and was slowly and painstakingly advanced to the point of understating the biological role of what initially was just an odd genomic feature. [ABSTRACT FROM AUTHOR]

Nitrogen is a critical element for algal growth and shifting its concentration above or below the optimum concentration may have a deleterious effect on algal cells. Antioxidants are one of the important factors that protect algal cells from stresses, e.g., nitrogen stress. The purpose of this study was to evaluate the biomass, pigments, antioxidant compounds and activities of two algal species, Arthrospira platensis (prokaryotic Cyanophyta) and Pseudochlorella pringsheimii (eukaryotic Chlorophyta) under hypo- and hyper-nitrogen concentrations. In general, the increase in the nitrogen concentrations of the nutrient medium (75 and 6-18 mM for A. platensis and P. pringsheimii, respectively) led to an increase in the biomass yield, pigments and other antioxidant contents. However, this increment was reversed by further N additions. The data showed that the prokaryotic alga ( A. platensis) can grow at relatively hyper-nitrogen concentrations rather than the eukaryotic one ( P. pringsheimii). The antioxidant enzyme activities for the both species were significantly stimulated with the relatively lower nitrogen concentrations, while increasing the N concentrations in the media decreased the enzyme activities. Despite the superiority of A. platensis as a potent antioxidants source, both algae showed high antioxidant levels compared to the synthetic antioxidant marker (butylated hydroxytoluene, BHT). [ABSTRACT FROM AUTHOR]