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This study investigates how cover crops (CC) and different application rates of glyphosate-based herbicide (GBH) may affect soil microbial communities. Our hypothesis was that the use of CC would promote the presence of certain microbial communities in soils and mitigate the potential impact of GBH on these communities. CC can promote biodiversity by increasing plant diversity in fields, while GBH may have non-target effects on species that utilize the shikimate pathway. Crop managements in an experimental field in Southern Québec (Canada) consisted in Glyphosate-based Herbicide (GBH) applications rates at 0.84, 1.67 and 3.33 L ha−1 in corn, soybean and wheat fields cultivated with Direct Seeding along with CC (DSCC) and at 3.33 L ha−1 in similar crops cultivated with direct seeding but without CC (DS). DSCC did not significantly impact microbial richness compared to DS, but did alter specific abundance among prokaryotes and eukaryotes. A permutational multivariate analysis revealed that the type of crop (soybean, wheat, maize) significantly influenced the composition of eukaryotic communities in 2018 and 2019, but not prokaryotic communities. Importantly, the study identifies a cross-effect between CC and GBH application rates suggesting that herbicide use in soybean plots can influence Anaeromyxobacter populations. Also, higher abundance of Enoplea and Maxilopoda were observed in plots with the lower application rate of GBH. Both eukaryotes group are known to be sensitive to crop management. These findings emphasize the need for a holistic approach to agricultural practices, considering the combined effects of both CC and GBH application rates on soil microbial health. Ultimately, the study calls for sustainable agricultural practices that preserve microbial diversity, which is essential for maintaining ecosystem services and soil health. [ABSTRACT FROM AUTHOR]

Background: Accurate taxonomic classification in genome databases is essential for reliable biological research and effective data sharing. Mislabeling or inaccuracies in genome annotations can lead to incorrect scientific conclusions and hinder the reproducibility of research findings. Despite advances in genome analysis techniques, challenges persist in ensuring precise and reliable taxonomic assignments. Existing tools for genome verification often involve extensive computational resources or lengthy processing times, which can limit their accessibility and scalability for large-scale projects. There is a need for more efficient, user-friendly solutions that can handle diverse datasets and provide accurate results with minimal computational demands. This work aimed to address these challenges by introducing a novel tool that enhances taxonomic accuracy, offers a user-friendly interface, and supports large-scale analyses. Results: We introduce a novel tool for the quality control and taxonomic classification tool of prokaryotic genomes, called DFAST_QC, which is available as both a command-line tool and a web service. DFAST_QC can quickly identify species based on NCBI and GTDB taxonomies by combining genome-distance calculations using MASH with ANI calculations using Skani. We evaluated DFAST_QC's performance in species identification and found it to be highly consistent with existing taxonomic standards, successfully identifying species across diverse datasets. In several cases, DFAST_QC identified potential mislabeling of species names in public databases and highlighted discrepancies in current classifications, demonstrating its capability to uncover errors and enhance taxonomic accuracy. Additionally, the tool's efficient design allows it to operate smoothly on local machines with minimal computational requirements, making it a practical choice for large-scale genome projects. Conclusions: DFAST_QC is a reliable and efficient tool for accurate taxonomic identification and genome quality control, well-suited for large-scale genomic studies. Its compatibility with limited-resource environments, combined with its user-friendly design, ensures seamless integration into existing workflows. DFAST_QC's ability to refine species assignments in public databases highlights its value as a complementary tool for maintaining and enhancing the accuracy of taxonomic data in genomic research. The web version is available at https://dfast.ddbj.nig.ac.jp/dqc/submit/, and the source code for local use can be found at https://github.com/nigyta/dfast_qc. [ABSTRACT FROM AUTHOR]

This study aimed to analyse the microbial biodiversity in ceriantharian tubes through shotgun metagenomics, to enhance the understanding of ecological dynamics in these microhabitats. We sampled two tubes of Ceriantheomorphe brasiliensis in Florianópolis (SC), and two tubes of Ceriantheopsis lineata in Alcatrazes archipelago (AK), South and Southeast Brazil, respectively. The environmental DNA from the tubes was extracted, amplified, and submitted to shotgun metagenomics sequencing on the Illumina HiSeq platform, and the biodiversity analysis was run using the Kraken2 software. Our results indicate that Ceriantharia-associated microbiomes likely harbour novel microbial diversity, as roughly only 8% of metagenomic reads were classified. Microbial composition was highly similar in both locations, with the Bacteria domain predominating, particularly the phyla Pseudomonadota and Actinomycetota. Nitrososphaerota was consistently the most common archaeal phylum in all samples. The bacterial classes Betaproteobacteria and Planctomycetia, and the archaeal class Nitrososphaeria were present in all four tubes, as were the bacterial family Pseudomonodaceae and the archaeal family Nitrosopumilaceae. Roseobactereaceae dominated alphaproteobacterial families from AK tubes, while Streptomycetaceae prevailed among actinobacterial families from SC tubes. The α-diversity indicates similar values between AK and SC samples, with slight distinctions favouring SC. β-diversity results show higher similarity within the same locations (AK or SC) than between different locations, highlighting spatial influence on microbial composition. To the best of our knowledge, this study is the first to address microbial composition found in ceriantharian tubes, using shotgun metagenomics, and our findings set up the scenario for a wider comprehension of these cnidarians as key holobionts in marine ecosystems. [ABSTRACT FROM AUTHOR]

Global warming and climate change are increasingly affecting the frequency and intensity of typhoons. The vertical mixing induced by typhoons enhances the availability of nutrients, subsequently influencing phytoplankton and prokaryotic ecology. However, research on the effects of typhoons on the ecology of phytoplankton and prokaryotes in the Yellow Sea (YS) is limited. This study examined the variations in phytoplankton and prokaryotic communities in response to typhoon-induced disturbances by comparing data from the YS in August 2020 (affected by Typhoon Bavi) with data from the typhoon-free period in August 2022. Post-typhoon observations revealed a decrease in water temperature and an increase in salinity within the surface mixed layer. Significantly higher concentrations of chlorophyll-a and pigments such as peridinin, fucoxanthin, alloxanthin, and chlorophyll-b were recorded in 2020, indicating an increase in phytoplankton biomass and shifts in its composition. Although prokaryotic heterotrophic production increased at most stations following the typhoon, changes in prokaryotic abundance and composition were less evident with only minor increases observed in Verrucomicrobiales and Euryarchaeota, potentially because of insufficient time for bacterial growth to manifest in increased abundance. Overall, the changes in phytoplankton and prokaryotic communities resembled those observed during the spring bloom, suggesting that typhoons can temporarily shift the pelagic ecosystem toward a bloom state during summer. [ABSTRACT FROM AUTHOR]

In the prokaryotic kingdom, protein phosphorylation serves as one of the most important posttranslational modifications (PTMs) and is involved in orchestrating a broad spectrum of biological processes. Here, we report an updated online server named the group-based prediction system for prokaryotic phosphorylation language model (GPS-pPLM), used for predicting phosphorylation sites (p-sites) in prokaryotes. For model training, two deep learning methods, a transformer and a deep neural network, were employed, and a total of 10 sequence features and contextual features were integrated. Using 44,839 nonredundant p-sites in 16,041 proteins from 95 prokaryotes, two general models for the prediction of O-phosphorylation and N-phosphorylation were first pretrained and then fine-tuned to construct 6 predictors specific for each phosphorylatable residue type as well as 134 species-specific predictors. Compared with other existing tools, the GPS-pPLM exhibits higher accuracy in predicting prokaryotic O-phosphorylation p-sites. Protein sequences in FASTA format or UniProt accession numbers can be submitted by users, and the predicted results are displayed in tabular form. In addition, we annotate the predicted p-sites with knowledge from 22 public resources, including experimental evidence, 3D structures, and disorder tendencies. The online service of the GPS-pPLM is freely accessible for academic research. [ABSTRACT FROM AUTHOR]

Ubiquitination is an evolutionary, ancient system of post-translational modification of proteins that occurs through a cascade involving ubiquitin activation, transfer, and conjugation. The maturation of this system has followed two main pathways. The first is the conservation of a universal structural fold of ubiquitin and ubiquitin-like proteins, which are present in both Archaea and Bacteria, as well as in multicellular Eukaryotes. The second is the rise of the complexity of the superfamily of ligases, which conjugate ubiquitin-like proteins to substrates, in terms of an increase in the number of enzyme variants, greater variation in structural organization, and the diversification of their catalytic domains. Here, we examine the diversity of the ubiquitination system among different organisms, assessing the variety and conservation of the key domains of the ubiquitination enzymes and ubiquitin itself. Our data show that E2 ubiquitin-conjugating enzymes of metazoan phyla are highly conservative, whereas the homology of E3 ubiquitin ligases with human orthologues gradually decreases depending on "molecular clock" timing and evolutionary distance. Surprisingly, Chordata and Echinodermata, which diverged over 0.5 billion years ago during the Cambrian explosion, share almost the same homology with humans in the amino acid sequences of E3 ligases but not in their adaptor proteins. These observations may suggest that, firstly, the E2 superfamily already existed in its current form in the last common metazoan ancestor and was generally not affected by purifying selection in metazoans. Secondly, it may indicate convergent evolution of the ubiquitination system and highlight E3 adaptor proteins as the "upper deck" of the ubiquitination system, which plays a crucial role in chordate evolution. [ABSTRACT FROM AUTHOR]

The vertical stratification of oxygen concentration in deep reservoirs impacts nutrient cycling and ecosystem biodiversity. The Serra da Mesa reservoir, the largest in Brazil, was studied to evaluate the structure and production of the prokaryote community at five depths. Using 3H leucine incorporation and fluorescent in situ hybridization (FISH), the study focused on different depths near the dam, particularly within the euphotic zone. The water column was characterized into oxic, transitional, and hypoxic layers based on dissolved oxygen concentration. The highest densities and biomasses of prokaryotes were found at the euphotic zone's depth limit, where bacterial production was low, suggesting inactive or slow-growing bacteria. Cell size differences and filamentous bacteria presence near the surface were observed, likely due to varying predation pressures. Prokaryote community composition differed across depths. At the subsurface level, with high dissolved organic carbon, alphaproteobacteria, betaproteobacteria, and Cytophaga–Flavobacter had similar densities, but the lowest bacterial biomass was recorded. The highest dissolved oxygen concentration depth had the lowest bacterial density, dominated by alphaproteobacteria and gammaproteobacteria. The study revealed that prokaryotic community structure and production vary with depth, indicating that microbial participation in layer dynamics is differentiated, with variations in abundance and distribution linked to oxygen concentrations. [ABSTRACT FROM AUTHOR]

Wetlands occupy up to 35% of the boreal biome in Russia, according to various estimates. Boreal bogs are global carbon sinks, accounting for more than 65% of the soil carbon stored in the wetland ecosystems of the world. The decomposition of plant residues is one of the most important components of the carbon cycle in wetland systems, while the violation of their fragile balance due to climate change increases the rate of mineralisation of organic matter and releases large amounts of carbon to the atmosphere. The biochemical processes occurring in a peat deposit determine the intensity of the destruction of organic matter and gas exchange. However, the microbial communities of the boreal ombrotrophic bogs, regulating those processes, are poorly studied. Hence, a study of the prokaryote communities of the peat deposits of the southern White Sea coastal ombrotrophic bogs (mostly spread in north-western Russia) was carried out. The taxonomic composition of archaea and bacteria sampled from the deposit's depth of 0–310 cm was studied using high-throughput sequencing of V4 sites of 16S rRNA gene by Illumina technology. As a result, 105 species belonging to 19 phylums were identified. The dominant specific phyla were Pseudomonadota, Acidobacteriota and Verrucomicrobiota, the non-specific phylum being Desulfobacterota. Various groups of methanogenic, methylotrophic and nitrogen-fixing microorganisms were identified. Shannon's biodiversity ranged from 3.5 to 4.6 and ChaO1 - from 232 to 351, decreasing within the depth. [ABSTRACT FROM AUTHOR]

Background: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system. Results: We uncovered distinct distribution patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as potentially host abundance- or phage/host ratio-driven phage population changes. Conclusions: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. 7mTZubWt51_LqpKWPutADa Video Abstract [ABSTRACT FROM AUTHOR]

Prokaryotes play a fundamental role in global ocean biogeochemical cycles. However, how the abundance and metabolic activity of ecologically distinct subgroups (i.e., high nucleic acid (HNA) and low nucleic acid (LNA) cells), and their regulating factors, change in response to changing marine environmental conditions remains poorly understood. Here, we delved into the time-evolving dynamic responses of the HNA and LNA prokaryotic subgroups to declining resource availability and selective grazing by protozoa by conducting a 73-day incubation experiment in a large-volume (117,000 L) macrocosm that facilitates community-level exploration. We found that the metabolic activity of the HNA subgroup was higher than that of the LNA subgroup when the macrocosm was resource replete but that the HNA subgroup declined more rapidly than the LNA subgroup as the resources became increasingly scarce, leading to a steadily increasing contribution of LNA cells to prokaryotic activity. Meanwhile, as resources in the macrocosm became limited, protozoan grazing preference shifted from the HNA to the LNA subgroup and the contributions of the LNA subgroup to the carbon flow within the macrocosm increased. The findings highlight the resilience of LNA cells in resource-limited environments, illuminate the critical role of selective grazing by protozoa in balancing distinct prokaryotic subgroups under changing resource conditions, and demonstrate the complex and adaptive interactions between protozoa and prokaryotes across diverse environmental contexts. [ABSTRACT FROM AUTHOR]

The concentration of viruses in sewage sludge is significantly higher (10–1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions. [ABSTRACT FROM AUTHOR]

Prokaryotic genomes are dynamic tapestries that are strongly influenced by mobile genetic elements (MGEs), including transposons (Tn's), plasmids, and bacteriophages. Of these, miniature inverted-repeat transposable elements (MITEs) are undoubtedly the least studied MGEs in bacteria and archaea. This review explores the diversity and distribution of MITEs in prokaryotes and describes what is known about their functional roles in the host and involvement in genomic plasticity and evolution. [ABSTRACT FROM AUTHOR]

Subtropical‐subpolar transition water is a potential domain for N2 fixation, but the understanding of N2 fixation in such waters remains incomplete. We simultaneously examined the N2 fixation activity and community structures of diazotrophs and all prokaryotes from the surface to just above the seafloor off Patagonia in the transitional region of the eastern South Pacific Ocean. N2 fixation activity was not detected in the surface waters, but was observed sporadically and only in subpolar bathypelagic waters (>1,000 m) at very low rates (0.02–0.06 nmol N L−1 d−1). By contrast, the nifH gene, a key gene involved in N2 fixation, was detected widely from the surface to the bottom waters. The majority of diazotrophs were classified as non‐cyanobacterial diazotrophs (NCDs), and the nifH amino acid sequences of major diazotrophs were similar to sequences detected in the Southern Ocean, the aphotic zone and sediment of other oceans, and estuarine waters, suggesting that the NCDs are distributed across diverse marine environments. The overall prokaryotic communities were generally similar to those in other open ocean regions at the phylum level (class level for Proteobacteria) and differed among water depths. Diazotrophs, in contrast, showed vertical and horizontal heterogeneity below the euphotic zone and little association with water depth, indicating a lack of cohesion within the community, which may characterize diazotroph community in the transitional surface water and aphotic zones. Elucidating this community heterogeneity may provide pivotal information about N2 fixation in these waters. Plain Language Summary: Marine N2 fixation is the main source of nitrogen to the oceans but was generally considered a local process that occurs primarily in the surface layers of tropical and subtropical oligotrophic waters. However, recent studies shows that N2 fixation occurs in diverse environments, including polar regions. The subtropical‐subpolar transition region has recently been recognized as a region where N2 fixation occurs, but studies of diazotrophy in this region have only just begun and information remains incomplete. In this study, diazotrophy in the transition region off Patagonia was examined throughout the water column. N2 fixation activity was sporadic in the deep waters of this region. By contrast, diazotrophs were detected from the surface to just above the seafloor. Unlike other prokaryotic communities, diazotrophic communities had heterogenous vertical and horizontal distribution below the euphotic zone. The heterogeneity of diazotrophs may be key to understanding N2 fixation in transitional surface and aphotic waters. Key Points: N2 fixation activity was detected sporadically and only in subpolar bathypelagic waters off western PatagoniaDiazotrophs were nearly omnipresent from the surface to just above the seafloorIn contrast to other prokaryotes, the vertical and horizontal distributions of diazotrophs were heterogeneous [ABSTRACT FROM AUTHOR]

Prokaryotes, the earliest forms of life on Earth, play crucial roles in global biogeochemical processes in virtually all ecosystems. The ever-increasing amount of prokaryotic genome sequencing data provides a wealth of information to examine fundamental and applied questions through systematic genome comparison. Genomic features, such as genome size and GC content, and taxonomy-centric genomic features of complete prokaryotic genomes (CPGs) are crucial for various fields of microbial research and education, yet they are often overlooked. Additionally, creating systematically curated datasets that align with research concerns is an essential yet challenging task for wet-lab researchers. In this study, we introduce CPGminer, a user-friendly tool that allows researchers to quickly and easily examine the genomic features and taxonomy of CPGs and curate genome datasets. We also provide several examples to demonstrate its practical utility in addressing descriptive questions. [ABSTRACT FROM AUTHOR]

The outer membrane of Gram-negative bacteria contains a variety of pore-forming structures collectively referred to as porins. Some of these are voltage dependent, but weakly so, closing at high voltages. Triplin, a novel bacterial pore-former, is a three-pore structure, highly voltage dependent, with a complex gating process. The three pores close sequentially: pore 1 at positive potentials, 2 at negative and 3 at positive. A positive domain containing 14 positive charges (the voltage sensor) translocates through the membrane during the closing process, and the translocation is proposed to take place by the domain entering the pore and thus blocking it, resulting in the closed conformation. This mechanism of pore closure is supported by kinetic measurements that show that in the closing process the voltage sensor travels through most of the transmembrane voltage before reaching the energy barrier. Voltage-dependent blockage of the pores by polyarginine, but not by a 500-fold higher concentrations of polylysine, is consistent with the model of pore closure, with the sensor consisting mainly of arginine residues, and with the presence, in each pore, of a complementary surface that serves as a binding site for the sensor. [ABSTRACT FROM AUTHOR]

The evolution of the mitochondria was a significant event that gave rise to the eukaryotic lineage and most large complex life. Central to the origins of the mitochondria was an endosymbiosis between prokaryotes. Yet, despite the potential benefits that can stem from a prokaryotic endosymbiosis, their modern occurrence is exceptionally rare. While many factors may contribute to their rarity, we lack methods for estimating the extent to which they constrain the appearance of a prokaryotic endosymbiosis. Here, we address this knowledge gap by examining the role of metabolic compatibility between a prokaryotic host and endosymbiont. We use genome-scale metabolic flux models from three different collections (AGORA, KBase, and CarveMe) to assess the viability, fitness, and evolvability of potential prokaryotic endosymbioses. We find that while more than half of host-endosymbiont pairings are metabolically viable, the resulting endosymbioses have reduced growth rates compared to their ancestral metabolisms and are unlikely to gain mutations to overcome these fitness differences. In spite of these challenges, we do find that they may be more robust in the face of environmental perturbations at least in comparison with the ancestral host metabolism lineages. Our results provide a critical set of null models and expectations for understanding the forces that shape the structure of prokaryotic life. [ABSTRACT FROM AUTHOR]

Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes. [ABSTRACT FROM AUTHOR]

Gram-negative bacteria have a large variety of channel-forming proteins in their outer membrane, generally referred to as porins. Some display weak voltage dependence. A similar trimeric channel former, named Triplin, displays very steep voltage dependence, rivaling that responsible for the electrical excitability of mammals, and high inter-subunit cooperativity. We report detailed insights into the molecular basis for these very unusual properties explored at the single-molecule level. By using chemical modification to reduce the charge on the voltage sensors, they were shown to be positively charged structures. Trypsin cleavage of the sensor eliminates voltage gating by cleaving the sensor. From asymmetrical addition of these reagents, the positively charged voltage sensors translocate across the membrane and are, thus, responsible energetically for the steep voltage dependence. A mechanism underlying the cooperativity was also identified. Theoretical calculations indicate that the charge on the voltage sensor can explain the rectification of the current flowing through the open pores if it is located near the pore mouth in the open state. All results support the hypothesis that one of the three subunits is oriented in a direction opposite to that of the other two. These properties make Triplin perhaps the most complex pore-forming molecular machine described to date. [ABSTRACT FROM AUTHOR]

The Santa Elena Ophiolite is a well-studied ultramafic system in Costa Rica mainly comprised of peridotites. Here, tropical climatic conditions promote active laterite formation processes, but the biogeochemistry of the resulting serpentine soils is still poorly understood. The aim of this study was to characterize the soil geochemical composition and microbial community of contrasting landscapes in the area, as the foundation to start exploring the biogeochemistry of metals occurring there. The soils were confirmed as Ni-rich serpentine soils but differed depending on their geographical location within the ophiolite area, showing three serpentine soil types. Weathering processes resulted in mountain soils rich in trace metals such as cobalt, manganese and nickel. The lowlands showed geochemical variations despite sharing similar landscapes: the inner ophiolite lowland soils were more like the surrounding mountain soils rather than the north lowland soils at the border of the ophiolite area, and within the same riparian basin, concentrations of trace metals were higher downstream towards the mangrove area. Microbial community composition reflected the differences in geochemical composition of soils and revealed potential geomicrobiological inputs to local metal biogeochemistry: iron redox cycling bacteria were more abundant in the mountain soils, while more manganese-oxidizing bacteria were found in the lowlands, with the highest relative abundance in the mangrove areas. The fundamental ecological associations recorded in the serpentine soils of the Santa Elena Peninsula, and its potential as a serpentinization endemism hotspot, demonstrate that is a model site to study the biogeochemistry, geomicrobiology and ecology of tropical serpentine areas. [ABSTRACT FROM AUTHOR]

Background: DIRs are mysterious protein that have the ability to scavenge free radicals, which, are highly reactive with molecules in their vicinity. What is even more fascinating is that they carry out from these highly unstable species, a selective reaction (i.e., stereoenantioselective) from a well-defined substrate to give a very precise product. Unfortunately, to date, only three products have been demonstrated following studies on DIRs from the plant world, which until now was the kingdom where these proteins had been demonstrated. Within this kingdom, each DIR protein has its own type of substrate. The products identified to date, have on the other hand, a strong economic impact: in agriculture for example, the biosynthesis of (+)-gossypol could be highlighted (a repellent antifood produced by the cotton plant) by the DIRs of cotton. In forsythia plant species, it is the biosynthesis of (−)-pinoresinol, an intermediate leading to the synthesis of podophyllotoxine (a powerful anicancerous agent) which has been revealed. Recently, a clear path of study, potentially with strong impact, appeared by the hypothesis of the potential existence of protein DIR within the genomes of prokaryotes. The possibility of working with this type of organism is an undeniable advantage: since many sequenced genomes are available and the molecular tools are already developed. Even easier to implement and working on microbes, of less complex composition, offers many opportunities for laboratory studies. On the other hand, the diversity of their environment (e.g., soil, aquatic environments, extreme environmental conditions (pH, temperature, pressure) make them very diverse and varied subjects of study. Identifying new DIR proteins from bacteria means identifying new substrate or product molecules from these organisms. It is the promise of going further in understanding the mechanism of action of these proteins and this will most likely have a strong impact in the fields of agricultural, pharmaceutical and/or food chemistry. Results: Our goal is to obtain as much information as possible about these proteins to unlock the secrets of their exceptional functioning. Analyzes of structural and functional genomic data led to the identification of the Pfam PF03018 domain as characteristic of DIR proteins. This domain has been further identified in the sequence of bacterial proteins therefore named as DIR-like (DIRL). We have chosen a multidisciplinary bioinformatic approach centered on bacterial genome identification, gene expression and regulation signals, protein structures, and their molecular information content. The objective of this study was to perform a thorough bioinformatic analysis on these DIRLs to highlight any information leading to the selection of candidate bacteria for further cloning, purification, and characterization of bacterial DIRs. Conclusions: From studies of DIRL genes identification, primary structures, predictions of their secondary and tertiary structures, prediction of DIRL signals sequences, analysis of their gene organization and potential regulation, a list of primary bacterial candidates is proposed. [ABSTRACT FROM AUTHOR]

Global warming may alter microbial ecosystem functions through reshaping of microbial diversities, compositions and interactions. Here, the community compositions, assembly processes and microbial interactions of prokaryotes (bacteria and archaea) were compared between the warming year of 2014 and 2016 in the Chukchi Sea. Our results indicated that prokaryotic diversity was significant higher in the warmer year of 2016. Furthermore, stochastic processes always dominated archaeal assembly processes, but bacterial assembly processes were mainly shaped by deterministic processes in 2016. And more keystones were detected in bacteria than that in archaea to maintain prokaryotic community stability. Both bacterial and archaeal community variations had significant correlations with environmental factors, although many of these factors (such as TN, TP, TOC and heavy metals) had not changed significantly from 2014 to 2016. Our study provides some new insights into microbial responses to climate warming in marine sediments. [ABSTRACT FROM AUTHOR]

Mangrove trees generally play important roles in protecting intertidal ecosystems. The mangrove root-associated sediments provide a repertoire of microbial communities that contribute to pivotal ecological functions in the system. In the present study, we used the high-throughput sequencing and PICRUSt-predicted functional information (based on 16S/18S rDNA profiles) to investigate the bacterial, archaeal, and fungal communities in two mangrove systems, located in the estuary of the Jiulong River (China), with different contaminated conditions and frequencies of human activity. Diverse distribution patterns for microbial communities were observed in six sediment samples collected from the two survey areas, which were found to be related mainly to the substrates in mangrove sediments. The sediments were predominated by relatively higher ratios of heterotrophic bacteria that participated in the degradation of organic matters, including phylum of Chloroflexi, Acidobacteriota, Desulfobacterota, and Proteobacteria. In addition, Crenarchaeota and Ascomycota presented the highest abundances of archaea and fungi, respectively. The relatively high concentrations of calcium, nitrogen, magnesium, and phosphorus in mangrove sediments correlated significantly with the microbial communities. In addition, although the potential functions were similar in the two sites based on COG and KEGG pathways, the abundances of enzymes involved in the degradation processes of cellulose and hemicellulose and the metabolism of nitrogen and sulfur presented distinctions. These results provide insights into the environmental conditions shaping microbial assemblies of the mangrove sediments under the impacts of human activities; for instance, a more abundant amount of calcium was found in urban areas in this study. [ABSTRACT FROM AUTHOR]

Canopy soils on large trees are important for supporting the lives of many canopy plants, and thereby increasing regional biodiversity. However, because of the less accessibility to canopy soils, there is insufficient knowledge on how canopy soils produce available nitrogen (N) for canopy plants through the activity of canopy soil microbes. Canopy soils usually have different soil properties from ground soils, so we hypothesized that canopy soils would have unique microbial communities compared to ground soils, but still provide available N for canopy plants. Here, we compared soil N availability, including net N mineralization and nitrification rate, and microbial communities between canopy soils (organic soils) collected at various heights of a large Cercidiphyllum japonicum tree and ground soils (organic and mineral soils) in a cool-temperate old-growth forest of Japan. The canopy soils had significantly different N availability (mass-based higher but volume-based lower) and microbial communities from the ground mineral soils. Among organic soils, the height of the soil had an impact on the microbial communities but not on the N availability, which agreed with our hypothesis. Despite the decrease in fungal abundance in the higher soils, the increase in certain components of the cellulose-decomposing fungi and oligotrophic bacteria may contribute to the available N production. Also, the abundance of ammonia-oxidizers did not change with the height, which would be important for the nitrification rate. Our study implied canopy soils could provide N to canopy plants partly through the functional redundancy within different microbial communities and constant population of ammonia-oxidizers. [ABSTRACT FROM AUTHOR]

Sirtuins are deacetylase enzymes widely distributed in all domains of life. Although for decades they have been related only to histones deacetylation in eukaryotic organisms, today they are considered global regulators in both prokaryotes and eukaryotes. Despite the important role of sirtuins in humans, the knowledge about bacterial sirtuins is still limited. Several proteomics studies have shown that bacterial sirtuins deacetylate a large number of lysines in vivo , although the effect that this deacetylation causes in most of them remains unknown. To date, only the regulation of a few bacterial sirtuin substrates has been characterized, being their metabolic roles widely distributed: carbon and nitrogen metabolism, DNA transcription, protein translation, or virulence. One of the most current topics on acetylation and deacetylation focuses on studying stoichiometry using quantitative LC-MS/MS. The results suggest that prokaryotic sirtuins deacetylate at low stoichiometry sites, although more studies are needed to know if it is a common characteristic of bacterial sirtuins and its biological significance. Unlike eukaryotic organisms, bacteria usually have one or few sirtuins, which have been reported to have closer phylogenetic similarity with the human Sirt5 than with any other human sirtuin. In this work, in addition to carrying out an in-depth review of the role of bacterial sirtuins in their physiology, a phylogenetic study has been performed that reveals the evolutionary differences between sirtuins of different bacterial species and even between homologous sirtuins. [ABSTRACT FROM AUTHOR]

Background: Characterizing phage–host interactions is critical to understanding the ecological role of both partners and effective isolation of phage therapeuticals. Unfortunately, experimental methods for studying these interactions are markedly slow, low-throughput, and unsuitable for phages or hosts difficult to maintain in laboratory conditions. Therefore, a number of in silico methods emerged to predict prokaryotic hosts based on viral sequences. One of the leading approaches is the application of the BLAST tool that searches for local similarities between viral and microbial genomes. However, this prediction method has three major limitations: (i) top-scoring sequences do not always point to the actual host; (ii) mosaic virus genomes may match to many, typically related, bacteria; and (iii) viral and host sequences may diverge beyond the point where their relationship can be detected by a BLAST alignment. Results: We created an extension to BLAST, named Phirbo, that improves host prediction quality beyond what is obtainable from standard BLAST searches. The tool harnesses information concerning sequence similarity and bacteria relatedness to predict phage–host interactions. Phirbo was evaluated on three benchmark sets of known virus–host pairs, and it improved precision and recall by 11–40 percentage points over currently available, state-of-the-art, alignment-based, alignment-free, and machine-learning host prediction tools. Moreover, the discriminatory power of Phirbo for the recognition of virus–host relationships surpassed the results of other tools by at least 10 percentage points (area under the curve = 0.95), yielding a mean host prediction accuracy of 57% and 68% at the genus and family levels, respectively, and drops by 12 percentage points when using only a fraction of viral genome sequences (3 kb). Finally, we provide insights into a repertoire of protein and ncRNA genes that are shared between phages and hosts and may be prone to horizontal transfer during infection. Conclusions: Our results suggest that Phirbo is a simple and effective tool for predicting phage–host relationships. [ABSTRACT FROM AUTHOR]

Early colonization and succession of soil microbial communities are essential for soil development and nutrient accumulation. Herein we focused on the changes in pioneer prokaryotic communities in rhizosphere and bulk soils along the high-elevation glacier retreat chronosequence, the northern Himalayas, Tibetan Plateau. Rhizosphere soils showed substantially higher levels of total organic carbon, total nitrogen, ammonium, and nitrate than bulk soils. The dominant prokaryotes were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Crenarchaeota, Bacteroidetes, and Planctomycetes, which totally accounted for more than 75% in relative abundance. The dominant genus Candidatus Nitrososphaera occurred at each stage of the microbial succession. The richness and evenness of soil prokaryotes displayed mild succession along chronosequene. Linear discriminant analysis effect size (LEfSe) analysis demonstrated that Proteobacteria (especially Alphaproteobacteria) and Actinobacteria were significantly enriched in rhizosphere soils compared with bulk soils. Actinobacteria, SHA_109, and Thermoleophilia; Betaproteobacteria and OP1.MSBL6; and Planctomycetia and Verrucomicrobia were separately enriched at each of the three sample sites. The compositions of prokaryotic communities were substantially changed with bulk and rhizosphere soils and sampling sites, indicating that the communities were dominantly driven by plants and habitat-specific effects in the deglaciated soils. Additionally, the distance to the glacier terminus also played a significant role in driving the change of prokaryotic communities in both bulk and rhizosphere soils. Soil C/N ratio exhibited a greater effect on prokaryotic communities in bulk soils than rhizosphere soils. These results indicate that plants, habitat, and glacier retreat chronosequence collectively control prokaryotic community composition and succession. [ABSTRACT FROM AUTHOR]

The remarkable diversity of sterol biosynthetic capacities described in living organisms is enriched at a fast pace by a growing number of sequenced genomes. Whereas analytical chemistry has produced a wealth of sterol profiles of species in diverse taxonomic groups including seed and non-seed plants, algae, phytoplanktonic species and other unicellular eukaryotes, functional assays and validation of candidate genes unveils new enzymes and new pathways besides canonical biosynthetic schemes. An overview of the current landscape of sterol pathways in the tree of life is tentatively assembled in a series of sterolotypes that encompass major groups and provides also peculiar features of sterol profiles in bacteria, fungi, plants, and algae. [ABSTRACT FROM AUTHOR]

Humans have coexisted with pathogenic microorganisms throughout its history of evolution. We have never halted the exploration of pathogenic microorganisms. With the improvement of genome-sequencing technology and the continuous reduction of sequencing costs, an increasing number of complete genome sequences of pathogenic microorganisms have become available. Genome annotation of this massive sequence information has become a daunting task in biological research. This paper summarizes the approaches to the genome annotation of pathogenic microorganisms and the available popular genome annotation tools for prokaryotes, eukaryotes and viruses. Furthermore, real-world comparisons of different annotation tools using 12 genomes from prokaryotes, eukaryotes and viruses were conducted. Current challenges and problems were also discussed. [ABSTRACT FROM AUTHOR]

Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0–20 cm, Middle: 20–40 cm, and Substratum: 40–100 cm) in a typical grassland by examining both distance–decay (DDRs) and species–area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (p <.05), with taxonomic turnover rates higher than phylogenetic ones. Specifically, the spatial turnover rates, β and z values, respectively, ranged from 0.016 ± 0.005 to 0.023 ± 0.005 and 0.065 ± 0.002 to 0.077 ± 0.004 across soil strata, and both increased with depth. Moreover, the prokaryotic community in grassland soils assembled mainly according to deterministic rather than stochastic mechanisms. By using normalized stochasticity ratio (NST) based on null model, the relative importance of deterministic ratios increased from 48.0 to 63.3% from Upper to Substratum, meanwhile a phylogenetic based method revealed average βNTI also increased with depth, from −5.29 to 19.5. Using variation partitioning and distance approaches, both geographic distance and soil properties were found to strongly affect biodiversity structure, the proportions increasing with depth, but spatial distance was always the main underlying factor. These indicated increasingly deterministic proportions in accelerating turnover rates for spatial assembly of prokaryotic biodiversity. Our study provided new insights on biogeography in different strata, revealing importance of assembly patterns and mechanisms of prokaryote communities in below‐surface soils. [ABSTRACT FROM AUTHOR]

Rickettsiales‐like organisms (RLOs) are intracellular bacteria that have been reported to be symbionts of over 60 species of bivalves and marine gastropod molluscs of aquaculture importance around the world. Morphologically, some of these prokaryotes are similar to bacteria from the order Rickettsiales, and in most cases, they form intracytoplasmic inclusions similar to those observed in bacteria of the family Anaplasmataceae. Genetically, only Candidatus Xenohaliotis californiensis (CXc), a parasite of several abalone species, has been classified as a member of the order Rickettsiales. The other two characterized RLOs are distantly related; one belongs to the same class (α‐proteobacteria), and the other belongs to the γ‐proteobacteria. Hyperparasitism of RLOs by bacteriophages has been reported in several species of mollusc and appears to have a negative effect on RLOs. The intracellular lifestyle of RLOs has been associated with cell alterations including hypertrophy and compression of the cytoplasmic organelles, and in most cases, no host reaction is observed by histology. In some cases, a high infection intensity of RLOs has been related to dysfunction of the affected organs that can result in disease, and in other cases, high burdens of RLOs have been associated with mortality, but most of these cases have yet to be confirmed. To date, only CXc has been confirmed as the aetiological agent of a chronic and potentially lethal disease of several abalone species known as withering syndrome. This disease is listed by the World Organization of Animal Health. With the ever‐increasing interest in preserving fisheries and expanding the aquaculture production of mollusc species, more efforts should be focused on the characterization and study of RLOs to elucidate the type of symbiosis they maintain with their host and determine when they are acting as true pathogens that should be subjected to control in aquaculture. This review provides an overview of the literature on RLOs that infect bivalves and gastropods of aquaculture importance, and we discuss the most important aspects of these unique prokaryotes. [ABSTRACT FROM AUTHOR]

Viruses are non-living, acellular entities, and the most abundant biological agents on earth. They are widely acknowledged as having the capacity to influence global biogeochemical cycles by infecting the bacterial and archaeal populations that regulate carbon and nutrient turnover. Evidence suggests that the majority of viruses in wetlands are bacteriophages, but despite their importance, studies on how viruses control the prokaryotic community and the concomitant impacts on ecosystem function (such as carbon cycling and greenhouse gas flux) in wetlands are rare. Here we investigate virus-prokaryote interactions in freshwater wetland ecosystems in the context of their potential influence on biogeochemical cycling. Specifically, we (1) synthesize existing literature to establish current understanding of virus-prokaryote interactions, focusing on the implications for wetland greenhouse gas dynamics and (2) identify future research priorities. Viral dynamics in freshwater wetlands have received much less attention compared to those in marine ecosystems. However, based on our literature review, within the last 10 years, viral ecology studies on freshwater wetlands have increased twofold. Despite this increase in literature, the potential implication of viral infections on greenhouse gas emission dynamics is still a knowledge gap. We hypothesize that the rate of greenhouse gas emissions and the pool of sequestered carbon could be strongly linked to the type and rate of viral infection. Viral replication mechanism choice will consequently influence the microbial efficiency of organic matter assimilation and thus the ultimate fate of carbon as a greenhouse gas or stored in soils. [ABSTRACT FROM AUTHOR]

Promoters are DNA regulatory elements located directly upstream or at the 5' end of the transcription initiation site (TSS), which are in charge of gene transcription initiation. With the completion of a large number of microorganism genomics, it is urgent to predict promoters accurately in bacteria by using the computational method. In this work, a sequence-based predictor named "iPro70-PseZNC" was designed for identifying sigma70 promoters in prokaryote. In the predictor, the samples of DNA sequences are formulated by a novel pseudo nucleotide composition, called PseZNC, into which the multi-window Z-curve composition and six local DNA structural properties are incorporated. In the 5-fold cross-validation, the area under the curve of receiver operating characteristic of 0.909 was obtained on our benchmark dataset, indicating that the proposed predictor is promising and will provide an important guide in this area. Further studies showed that the performance of PseZNC is better than it of multi-window Z-curve composition. For the sake of convenience for researchers, a user-friendly online service was established and can be freely accessible at http://lin.uestc.edu.cn/server/iPro70-PseZNC. The PseZNC approach can be also extended to other DNA-related problems. [ABSTRACT FROM AUTHOR]

In bacterial DNA, there are specific sequences of nucleotides called promoters that can bind to the RNA polymerase. Sigma70 (σ70) is one of the most important promoter sequences due to its presence in most of the DNA regulatory functions. In this paper, we identify the most effective and optimal sequence-based features for prediction of σ70 promoter sequences in a bacterial genome. We used both short-range and long-range DNA sequences in our proposed method. A very small number of effective features are selected from a large number of the extracted features using multi-window of different sizes within the DNA sequences. We call our prediction method iPro70-FMWin and made it freely accessible online via a web application established at http://ipro70.pythonanywhere.com/server for the sake of convenience of the researchers. We have tested our method using a standard benchmark dataset. In the experiments, iPro70-FMWin has achieved an area under the curve of the receiver operating characteristic and accuracy of 0.959 and 90.57%, respectively, which significantly outperforms the state-of-the-art predictors. [ABSTRACT FROM AUTHOR]

Sugars will eventually be exported transporters (SWEETs) and SemiSWEETs represent a family of sugar transporters in eukaryotes and prokaryotes, respectively. SWEETs contain seven transmembrane helices (TMHs), while SemiSWEETs contain three. The functions of SemiSWEETs are less studied. In this perspective article, we analyzed the diversity and conservation of SemiSWEETs and further proposed the possible functions. 1,922 SemiSWEET homologs were retrieved from the UniProt database, which is not proportional to the sequenced prokaryotic genomes. However, these proteins are very diverse in sequences and can be classified into 19 clusters when >50% sequence identity is required. Moreover, a gene context analysis indicated that several SemiSWEETs are located in the operons that are related to diverse carbohydrate metabolism. Several proteins with seven TMHs can be found in bacteria, and sequence alignment suggested that these proteins in bacteria may be formed by the duplication and fusion. Multiple sequence alignments showed that the amino acids for sugar translocation are still conserved and coevolved, although the sequences show diversity. Among them, the functions of a few amino acids are still not clear. These findings highlight the challenges that exist in SemiSWEETs and provide future researchers the foundation to explore these uncharted areas. [ABSTRACT FROM AUTHOR]

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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]

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]

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]

Arsenic, which is a major contaminant of many aquatic ecosystems worldwide, is responsible for serious public health issues. However, life has evolved various strategies for coping with this toxic element. In particular, prokaryotic organisms have developed processes enabling them to resist and metabolize this chemical. Studies based on genome sequencing and transcriptome, proteome and metabolome profiling have greatly improved our knowledge of prokaryotes' metabolic potential and functioning in contaminated environments. The increasing number of genomes available and the development of descriptive and comparative approaches have made it possible not only to identify several genetic determinants of the arsenic metabolism, but also to elucidate their phylogenetic distribution and their modes of regulation. In addition, studies using functional genomic tools have established the pleiotropic character of prokaryotes' responses to arsenic, which can be either common to several species or species-specific. These approaches also provide promising means of deciphering the functioning of microbial communities including uncultured organisms, the genetic transfers involved and the possible occurrence of metabolic interactions as well as the evolution of arsenic resistance and metabolism. [ABSTRACT FROM AUTHOR]

The discovery of fossil melanosomes has resulted in a wealth of research over the last 7 years, notably the reconstruction of colour in dinosaurs and fossil mammals. In spite of these discoveries some authors persist in arguing that the observed microbodies could represent preserved bacteria. They contend that bacteria fossilise easily and everywhere, which means that one can never be certain that a microbody is a melanosome without an extraordinary burden of evidence. However, this critique mischaracterises the morphological and structural evidence for interpreting microbodies as fossil melanosomes, and hence the basis for using them in reconstructing prehistoric colours. The claims for bacterial omnipresence in the fossil record are themselves not supported, thus tipping the scales strongly towards melanosomes in the bacteria-versus-melanosome controversy. [ABSTRACT FROM AUTHOR]

Orthologs are widely used for phylogenetic analysis of species; however, identifying genuine orthologs among distantly related species is challenging, because genes obtained through horizontal gene transfer (HGT) and out-paralogs derived from gene duplication before speciation are often present among the predicted orthologs. We developed a program, “Ortholog-Finder,” to obtain ortholog data sets for performing phylogenetic analysis by using all open-reading frame data of species. The program includes five processes forminimizing the effects of HGT and out-paralogs in phylogeny construction: 1) HGT filtering: Genes derived from HGT could be detected and deleted from the initial sequence data set by examining their base compositions. 2)Out-paralog filtering:Outparalogs aredetected anddeleted fromthe data setbasedonsequence similarity.3)Classificationof phylogenetic trees: Phylogenetic trees generated for ortholog candidates are classified as monophyletic or polyphyletic trees. 4) Tree splitting: Polyphyletic trees are bisected to obtain monophyletic trees and remove HGT genes and out-paralogs. 5) Threshold changing: Out-paralogs are further excluded from the data set based on the difference in the similarity scores of genuine orthologs and out-paralogs.Weexaminedhow out-paralogs and HGTs affected phylogenetic trees constructed for species based on ortholog data sets obtained by Ortholog-Finder with the use of simulation data, andwe determined the effects of confounding factors.Wethen used Ortholog-Finder in phylogeny construction for 12 Gram-positive bacteria from two phyla and validated each node of the constructed tree by comparison with individually constructed ortholog trees. [ABSTRACT FROM AUTHOR]

We examined the effects of mass sedimentation events caused by the 2011 off the Pacific coast of Tohoku Earthquake on abundances and vertical distributions of prokaryotes and metazoan meiofauna in sediments, using sediment cores collected from eight bathyal stations off Tohoku 1 year after the M9.0 earthquake. Event deposits 1-7 cm thick were observed at the topmost part of the sediment cores at all sampling stations. At some stations, prokaryotic cell abundances were lower in the surface event-deposit layers compared to those in deeper sediments. These variations were explained by environmental parameters such as a dimensionless sorting factor and mean grain size, suggesting that turbidite sedimentation affected prokaryotic cell abundances. Nematodes had anomalously higher subsurface abundances at the stations where subsurface peak prokaryotic cell numbers were observed, whereas copepods always showed peak densities in the sediment surface layer. Although there are no available data for prokaryotic cell abundances and meiofaunal densities before the earthquake from the same sites, it is likely that the subsurface peaks in prokaryotic cell numbers and nematode densities resulted from the sedimentation events. The effects of sedimentation events on the organisms were observed 1 year after the earthquake, indicating that episodic sedimentation events on scales of several centimeters have a large effect on small organisms inhabiting sediments. [ABSTRACT FROM AUTHOR]