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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]

Argentina stands as the seventh-largest wine producer. Its broad geographical and climatic diversity contributes to the production of wines with distinctive regional characteristics. Microorganisms associated with vines play a crucial role in wine quality. Recent studies have revealed significant differences in microbial communities between grape varieties and vineyard locations. In this work, we conducted a comprehensive examination of the diversity of prokaryotic microorganisms in the rhizosphere of vineyards located in three wine regions of Argentina. We used next-generation sequencing methods, concentrating the analysis on two relevant cultivars, Malbec and Cabernet Sauvignon. Both varietals have attracted significant interest in recent research given their distinctive characteristics, which vary according to the geographic growing region. The soil physicochemical properties of the vineyards analysed, were evaluated by principal component analysis, and clustering analysis, allowing us to identify differences among them. Despite no significant variations were observed between Malbec and Cabernet-Sauvignon vineyards, significant differences in microbial diversity were observed among the analysed locations. Taxonomic identification showed distinct microbial compositions across regions, with notable differences in abundance at the family level. Canonical correspondence analysis indicated correlations between soil physicochemical properties and microbial families, highlighting the influence of soil characteristics on microbiota composition. These differences in microbial populations set a site-specific prokaryotic profile that could be used as an identifying signature. Comprehending these interactions is essential for improving vineyard management techniques, ultimately shaping the sensory characteristics of wines crafted in diverse regions.

Abstract Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.

Abstract 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. Video Abstract

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]

Abstract Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40–60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.

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.

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 bacterial chromosome is both highly supercoiled and bound by an ensemble of proteins and RNA, causing the DNA to form a compact structure termed the nucleoid. The nucleoid serves to condense, protect, and control access to the bacterial chromosome through a variety of mechanisms that remain incompletely understood. The nucleoid is also a dynamic structure, able to change both in size and composition. The dynamic nature of the bacterial nucleoid is particularly apparent when studying the effects of various stresses on bacteria, which require cells to protect their DNA and alter patterns of transcription. Stresses can lead to large changes in the organization and composition of the nucleoid on timescales as short as a few minutes. Here, we summarize some of the recent advances in our understanding of how stress can alter the organization of bacterial chromosomes. [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]

ABSTRACT This paper presents two low-cost hands-on activities designed to enhance student understanding and address the pedagogical challenges faced by microbiology professors in teaching concepts related to cell structure and gene regulation. In the first activity, we used Shrinky Dinks and Jeopardy-style game questions to explore the differences between prokaryotic and eukaryotic cells. Students have to collect pieces and physically build their cell models. The second activity uses origami organelles sets from Edvotek to illustrate the regulation of gene expression in the lac and trp operons, incorporating mutation scenarios for analysis. The intended audience comprises undergraduate students in microbiology, including biology, pre-medical studies, and health profession majors. The activities were deployed in three microbiology lectures, and students were surveyed. Students’ feedback highlights the efficacy of the hands-on approach and increased class participation, as two of the recurring words in the students’ survey were “helpful” and “fun.”

ABSTRACT Microbiomes are integral to ecological health and human well-being; however, their ecological and evolutionary drivers have not been systematically investigated, especially in urban park ecosystems. As microbes have different levels of tolerance to environmental changes and habitat preferences, they can be categorized into habitat generalists and specialists. Here, we explored the ecological and evolutionary characteristics of both prokaryotic and microeukaryotic habitat generalists and specialists from six urban parks across five habitat types, including moss, soil, tree hole, water, and sediment. Our results revealed that different ecological and evolutionary processes maintained and regulated microbial diversity in urban park ecosystems. Under ecological perspective, community assembly of microbial communities was mainly driven by stochastic processes; however, deterministic processes were higher for habitat specialists than generalists. Microbial interactions were highly dynamic among habitats, and habitat specialists played key roles as module hubs in intradomain networks. In aquatic interdomain networks, microeukaryotic habitat specialists and prokaryotic habitat specialists played crucial roles as module hubs and connectors, respectively. Furthermore, analyzing evolutionary characteristics, our results revealed that habitat specialists had a much higher diversification potential than generalists, while generalists showed shorter phylogenetic branch lengths as well as larger genomes than specialists. This study broadens our understanding of the ecological and evolutionary features of microbial habitat generalists and specialists in urban park ecosystems across multi-habitat.IMPORTANCEUrban parks, as an important urban greenspace, play essential roles in ecosystem services and are important hotspots for microbes. Microbial diversity is driven by different ecological and evolutionary processes, while little is currently known about the distinct roles of ecological and evolutionary features in shaping microbial diversity in urban park ecosystems. We explored the ecological and evolutionary characteristics of prokaryotic and microeukaryotic habitat generalists and specialists in urban park ecosystems based on a representative set of different habitats. We found that different ecological and evolutionary drivers jointly maintained and regulated microbial diversity in urban park microbiomes through analyzing the community assembly process, ecological roles in hierarchical interaction, and species diversification potential. These findings significantly advance our understanding regarding the mechanisms governing microbial diversity in urban park ecosystems.

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]

Abstract 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.

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]

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.

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]

Abstract 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.

Coastal sediments are a critical domain for carbon sequestration and are profoundly impacted by human activities. Therefore, it is essential to understand the structure and components of benthic autotrophs that play a crucial role in carbon sequestration processes, as well as the influence of anthropogenic activities on their communities. This study utilized an urban estuary, an industrial sea bay, a maricultural sea region, and two mangrove coastlines within the coastal areas of Guangdong Province, China. The micro-benthos in these environments, including prokaryotes and eukaryotes, were identified through high-throughput sequencing of 16S rRNA and 18S rRNA genes. The findings show that the autotrophic composition was altered by the interactions of anthropogenic heavy metals (Cd and Zn) and micro-eukaryotes (protazoa, metazoa, and parasitic organisms). Industrial pollution reduced the abundance of both prokaryotic and eukaryotic autotrophs. Mangroves induced a substantial transformation in the sediment eukaryotic and prokaryotic composition, increasing the proportion of autotrophs, notably sulfur-oxidizing and iron-oxidizing bacteria and microalgae. This alteration suggests an increase in specific sulfur and iron cycling with simultaneous carbon sequestration within mangrove sediments. These results indicate that anthropogenic activities affect sediment carbon sequestration by altering autotrophic assemblages along coastlines, thereby inducing consequential shifts in overall elemental cycling processes. [Display omitted] • Heavy metals (Cu and Zn) determined the benthic prokaryotic autotrophs. • Mangrove sediment enhanced the functional autotrophs of S/Fe-oxidizer and algae. • Industrial coastal sediment inhibited the growth of autotrophs. • The changed of functional autotrophs would finally affect the C, N, S, Fe cycling processes. [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]

Marine microorganisms are involved in a variety of biogeochemical cycles and live in diverse ecological communities where they interact with each other and with other organisms to guarantee ecosystem functions. The present study focused on a shallow marine environment located in Ría de Vigo (NW, Spain), where sediment and size-fractionated plankton samples were collected from 2016 to 2018. DNA metabarcoding was used to describe the eukaryote and prokaryote composition and diversity in sediments and plankton and to depict possible associations among the most frequent and abundant organisms by co-occurrence network analysis. High eukaryote and prokaryote diversity indices were obtained in all compartments. Significant differences among eukaryote and prokaryote communities were found between sediment and plankton samples, with a high percentage of exclusive operational taxonomic units (OTUs) associated with each compartment, especially from sediment. Despite these differences, shared taxa between water and sediment were also obtained, suggesting a relatively meaningful exchange of organisms between both environmental compartments. Significant co-occurrences were mainly obtained between prokaryotes (41%), followed by eukaryotes–prokaryotes (32%) and between eukaryotes (27%). The abundant and strong positive correlations between organisms, including representatives from the sediment and the water column, suggested an essential role of biotic interactions as community-structuring factors in shallow waters where beneficial associations likely prevail. This study provides a novel approach for the detailed description of the eukaryote and prokaryote diversity and co-occurrence patterns in a shallow marine area, including both the sediment and different water-size fractions. The high diversity obtained and the detection of predominantly coexisting interactions among organisms from sediment and the overlying water column suggest a movement of species between both habitats and therefore confirm the importance of integratively studying shallow marine ecosystems.

The virus-to-prokaryote ratio (VPR) has been used in many ecosystems to study the relationship between viruses and their hosts. While high VPR values indicate a high rate of prokaryotes' cell lysis, low values are interpreted as a decrease in or absence of viral activity. Salar de Huasco is a high-altitude wetland characterized by a rich microbial diversity associated with aquatic sites like springs, ponds, streams and a lagoon with variable physicochemical conditions. Samples from two ponds, Poza Rosada (PR) and Poza Verde (PV), were analyzed by epifluorescence microscopy to determine variability of viral and prokaryotic abundance and to calculate the VPR in a dry season. In addition, to put Salar de Huasco results into perspective, a compilation of research articles on viral and prokaryotic abundance, VPR, and metadata from various Southern hemisphere ecosystems was revised. The ecosystems were grouped into six categories: high-altitude wetlands, Pacific, Atlantic, Indian, and Southern Oceans and Antarctic lakes. Salar de Huasco ponds recorded similar VPR values (an average of 7.4 and 1.7 at PR and PV, respectively), ranging from 3.22 to 15.99 in PR. The VPR variability was associated with VA and chlorophyll a, when considering all data available for this ecosystem. In general, high-altitude wetlands recorded the highest VPR average (53.22 ± 95.09), followed by the Oceans, Southern (21.91 ± 25.72), Atlantic (19.57 ± 15.77) and Indian (13.43 ± 16.12), then Antarctic lakes (11.37 ± 15.82) and the Pacific Ocean (6.34 ± 3.79). Physicochemical variables, i.e., temperature, conductivity, nutrients (nitrate, ammonium, and phosphate) and chlorophyll a as a biological variable, were found to drive the VPR in the ecosystems analyzed. Thus, the viral activity in the Wetland followed similar trends of previous reports based on larger sets of metadata analyses. In total, this study highlights the importance of including viruses as a biological variable to study microbial temporal dynamics in wetlands considering their crucial role in the carbon budgets of these understudied ecosystems in the southern hemisphere.

Abstract Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo .

Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biotas on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4000 km in both alpine and temperate biotas. Prokaryotic similarities increased over geographic distance after tipping points of 1760–1920 km, generating a significant U-shape pattern. Such pattern was likely due to decreased disparities in environmental heterogeneity over geographic distance when across biotas, supported by three lines of evidences: (1) prokaryotic similarities still decreased with the environmental distance, (2) environmental selection dominated prokaryotic assembly, and (3) short-term environmental heterogeneity followed the U-shape pattern spatially, especially attributed to dissolved nutrients. In sum, these results demonstrate that environmental selection overwhelmed the geographic ‘distance’ effect when across biotas, overturning the previously well-accepted geographic pattern for microbes on a large scale.

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]

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.

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.