In conclusion, trypsin digestion of in-gel proteins was the optimal method for the meta-proteomic pipeline analyzing rumen microbial ureases. This pipeline provides a guide for targeted meta-proteomic analyses in other ecosystems.Species of the genus Shewanella are widespread in nature in various habitats, however, little is known about phages affecting Shewanella sp. Here, we report the isolation of phages from diverse freshwater environments that infect and lyse strains of Shewanella oneidensis and other Shewanella sp. Sequence analysis and microscopic imaging strongly indicate that these phages form a so far unclassified genus, now named Shewanella phage Thanatos, which can be positioned within the subfamily of Tevenvirinae (Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tevenvirinae). We characterized one member of this group in more detail using S. oneidensis MR-1 as a host. Shewanella phage Thanatos-1 possesses a prolate icosahedral capsule of about 110 nm in height and 70 nm in width and a tail of about 95 nm in length. selleck chemical The dsDNA genome exhibits a GC content of about 34.5%, has a size of 160.6 kbp and encodes about 206 proteins (92 with an annotated putative function) and two tRNAs. Out of those 206, MS analyses identified about 155 phage proteins in PEG-precipitated samples of infected cells. Phage attachment likely requires the outer lipopolysaccharide of S. oneidensis, narrowing the phage’s host range. Under the applied conditions, about 20 novel phage particles per cell were produced after a latent period of approximately 40 min, which are stable at a pH range from 4 to 12 and resist temperatures up to 55°C for at least 24 h. Addition of Thanatos to S. oneidensis results in partial dissolution of established biofilms, however, early exposure of planktonic cells to Thanatos significantly enhances biofilm formation. Taken together, we identified a novel genus of Myophages affecting S. oneidensis communities in different ways.With increasing resolution of microbial diversity at the genomic level, experimental and modeling frameworks that translate such diversity into phenotypes are highly needed. This is particularly important when comparing drug-resistant with drug-sensitive pathogen strains, when anticipating epidemiological implications of microbial diversity, and when designing control measures. Classical approaches quantify differences between microbial strains using the exponential growth model, and typically report a selection coefficient for the relative fitness differential between two strains. The apparent simplicity of such approaches comes with the costs of limiting the range of biological scenarios that can be captured, and biases strain fitness estimates to polarized extremes of competitive exclusion. Here, we propose a mathematical and statistical framework based on the Lotka-Volterra model, that can capture frequency-dependent competition between microbial strains within-host and upon transmission. As a proof-of-concept, the model is applied to a previously-published dataset from in-vivo competitive mixture experiments with influenza strains in ferrets (McCaw et al., 2011). We show that for the same data, our model predicts a scenario of coexistence between strains, and supports a higher bottleneck size in the range of 35-145 virions transmitted from donor to recipient host. Thanks to its simplicity and generality, such framework could be applied to other ecological scenarios of microbial competition, enabling a more complex and nuanced view of possible outcomes between two strains, beyond competitive exclusion.SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus responsible for the current COVID-19 (coronavirus disease 2019) pandemic, which has hit the world since December 2019. It has spread to about 216 countries worldwide, affecting more than 21.7 million people so far. Although clinical trials of a number of promising antiviral drugs and vaccines against COVID-19 are underway, it is hard to predict how successful these drug- or vaccine-based therapeutics are eventually going to be in combating COVID-19 because most of such therapeutic strategies have failed against human coronaviruses such as SARS-CoV and MERS-CoV (Middle East respiratory syndrome coronavirus) responsible for similar pandemics in the past. In that context, we would like to bring to scientific attention another group of endogenous regulatory molecules, the small non-coding RNAs, especially the microRNAs, which are found to regulate critical cellular pathways in a number of disease conditions, including RNA viral infections. This review will focus on understanding the effect of altered microRNA expression during coronavirus-mediated infections and how it may provide clues for further exploring the pathogenesis of SARS-CoV-2, with a view of developing RNAi-based therapeutics and biomarkers against COVID-19.Leaves and roots harbor taxonomically diverse bacterial assemblages which enhance plant growth and performance by increasing nutrient supply and resistance to stress. An extensive investigation of bacterial diversity and composition between leaf and root microbiota of 15 bamboo species differing in rhizome types, lifeforms and sampling sites were conducted by high-through sequencing. The alpha diversity between leaf and root microbiota was not significantly different, whereas, their beta diversity differed remarkably. Niche specialization mainly in species from Actinobacteria was detected which prefer to colonize in roots than leaves. Community structure of leaf microbiota was highly resembled, however, the phylogeny inferred by host’s chloroplast data was incongruent with microbiota dendrogram, indicating that phylosymbiosis didn’t occur in bamboos and their associated microbiota. Large overlap in functional profiling of leaf and root-associated microbiota was found. Accordingly, we proposed that environmental conditions, structural variation and physiological differences between leaves and roots worked collaboratively for divergence of bamboo microbiota. This study confers to a robust knowledge of bamboo-microbe interaction and provides a list of bacterial lineages for investigation into specific plant-microbe interaction information of which could be used to enhance agricultural and forest productivity.Leaf-cutter ants in the genus Atta are dominant herbivores in the Neotropics. While most species of Atta cut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12 Atta fungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. Differences between community composition and functional capacity of the bacteria in the two types of fungus gardens reflect differences in the substrates that the ants incorporated. These results show that different substrate inputs matter for fungus garden bacteria and shed light on the potential role of bacteria in mediating the ants‘ transition to the use of a novel substrate.The current trend of increasing input of terrestrially derived dissolved organic carbon (DOC) to boreal freshwater systems is causing increased levels of carbon dioxide (CO2) supersaturation and degassing. Phosphorus (P) is often the most limiting nutrient for bacterial growth and would thus be expected to increase overall mineralization rates and CO2 production. However, high carbon (C) to P ratios of terrestrially derived DOC could also cause elevated cell-specific respiration of the excess C in heterotrophic bacteria. Using data from a survey of 75 Scandinavian lakes along an ecosystem gradient of DOC, we estimated in situ CO2 production rates. These rates showed a unimodal response with DOC-specific CO2 production negatively related to DOCtotal phosphorus (TP) ratio, and a turning point at 5 mg C L-1, indicating higher DOC turnover rates in productive than in unproductive lakes. To further assess the dependency of bacterial respiration (BR) on DOC and P, we monitored CO2 production in incubations of water kinetics.Arsenic (As) is a metalloid that occurs widely in the environment. The biological oxidation of arsenite [As(III)] to arsenate [As(V)] is considered a strategy to reduce arsenic toxicity and provide energy. In recent years, research interests in microbial As(III) oxidation have been growing, and related new achievements have been revealed. This review focuses on the highlighting of the novel regulatory mechanisms of bacterial As(III) oxidation, the physiological relevance of different arsenic sensing systems and functional relationship between microbial As(III) oxidation and those of chemotaxis, phosphate uptake, carbon metabolism and energy generation. The implication to environmental bioremediation applications of As(III)-oxidizing strains, the knowledge gaps and perspectives are also discussed.Nowadays, contamination by polycyclic aromatic hydrocarbons (PAHs) has become a serious problem all over the world; in particular, high-molecular-weight PAHs (HWM PAHs, four to seven rings) are more harmful to human health and environment due to their more complex structure and metabolic pathway. Biodegradation of PAHs with six or more rings, such as indeno[1,2,3-cd]pyrene (IcdP), was rarely described. An IcdP-degrading strain, Rhodococcus aetherivorans IcdP1, was isolated from HWM PAH-contaminated soil. It could grow on and efficiently degrade various HWM PAHs, such as IcdP, benzo[a]pyrene, and benzo[j]fluoranthene. It showed highest degrading ability toward IcdP (> 70% within 10 days). The IcdP degradation was initiated by ring hydroxylation with multiple pathways, including the hydroxylation at the 1,2 and 7,8 positions, according to the relevant metabolites detected, e.g., cyclopenta[cd]pyrene-3,4-dicarboxylic acid and 2,3-dimethoxy-2,3-dihydrofluoranthene. The transcriptional patterns of the genes encoding ring-hydroxylating oxygenases (RHOs) and cytochrome P450 monooxygenases (CYP450s) under the induction of IcdP, pyrene, and benzo[b]fluoranthene (BbF) were compared to determine the key initial RHOs in the conversion of IcdP. The expression of genes encoding RHOs 1892-1894, 1917-1920, and 4740-4741 was induced strictly by IcdP, and the amino acid sequences of these proteins showed very low identities with their homologs. These results suggested that IcdP was degraded through a dioxygenation-initiated metabolism pattern, and RHOs 1892-1894, 1917-1920, and 4740-4741 responded to the initial ring cleavage of IcdP through 1,2-dihydrodiol or 7,8-dihydrodiol. The studies would contribute to the understanding of the molecular mechanism of initial degradation of IcdP.