Environmental microbiology最新文献

Viruses are among the most abundant and diverse biological entities on Earth. Over the past decades, metagenomic sequencing has revealed thousands of viral genomes. However, viral isolation methods remain indispensable for discovering viruses that are missed by metagenomic sequencing due to limitations like low abundance (1, 2). Here, a novel phage, vB_PshM_Y4, which infects Pseudoalteromonas shioyasakiensis, an economically important, opportunistic marine pathogen was isolated. A comparison of vB_PshM_Y4 with over 15 million viral genomes, including both cultivated and uncultivated viruses in the NCBI and IMG/VR v4 datasets, found no closely related genome. This study provides evidence that traditional isolation methods can detect viruses that cannot be identified through metagenomic sequencing. In addition, a comparison of virus isolates deposited in the NCBI database with uncultured viruses in the IMG/VR viral database shows that approximately only half of the isolates can be detected using metagenomic approaches. Notably, viruses that are not able to be detected by metagenomic sequencing often exhibit low abundance and possess unique genomes. These results suggest that traditional viral isolation methods remain important for obtaining rare, low-abundance viruses and underscore the significance of traditional experimental methods in the era of metagenomes.

Heterotrophic nanoflagellates (HNF) are a key component of the microbial food webs, playing an essential role in nutrient recycling and energy transfer in aquatic ecosystems. They have been typically considered to be bacterivores, but they can also be omnivorous (feeding on prokaryotes and other eukaryotes) and predatory grazers (feeding on other eukaryotes). Here, we combine CARD-FISH with both short and long-amplicon sequencing to resolve the dynamics of key HNF groups during two high-frequency sampling campaigns in spring (March–May) and autumn (September–November) phytoplankton blooms in the coastal waters of the Baltic Sea. This approach allowed us to resolve the microbial food web dynamics within HNF communities at the phylotype level at time scales relevant to HNF duplication times. Omnivorous katablepharids and predatory MAST-2 dominated the HNF community, especially in spring. Bacterivorous groups (e.g., MAST-1, CRY1) were less abundant. Long-read sequencing revealed distinct seasonal shifts in dominant phylotypes, with Katablepharis sp. and MAST-2D peaking in spring, while other lineages became more prominent in summer and autumn. The high abundance of omnivorous HNF, compared to bacterivores, highlights their key role both as grazers of bacteria and flagellates, and as a food source for predatory and omnivorous ciliates.

The branching green macroalga Cladophora glomerata and its epiphytic microbiome dominate summer biomass in the Eel River, a Northern California river under Mediterranean (summer drought, winter rain) seasonality. Green Cladophora streamers proliferate in early summer, then change to yellow and then red-brown as epiphyte loads increase. We characterised successional changes in epiphytic bacteria on Cladophora, examining both community composition and growth rates, using quantitative Stable Isotope Probing (qSIP) and 16S rRNA gene amplicon sequencing. The number of bacterial taxa increased with succession while growth rates peaked in the middle stage. NanoSIMS imaging confirmed high sulphur (S) concentrations in Cladophora cell walls relative to surrounding biomass, coinciding with a bloom of sulphur bacteria (bacteria that reduce or oxidise sulphur/sulphates). In general, relative abundances and growth rates were independent, indicating that either metric alone is insufficient for understanding how taxonomy and functional groups affect ecosystem processes. For instance, the relative abundance of nitrogen fixers peaked in the late summer when their relative growth rates were slowest. Such patterns may be driven by space competition limiting growth. Together, changes in abundance and relative growth rates suggest different limiting factors for different functional groups in the Cladophora microbiome at multiple successional stages.

Endozoicomonas is an omnipresent marine bacterial genus, associated with various marine organisms, that contributes to host health, nutrient cycling and disease resistance. Nonetheless, its genomic features remain poorly characterised due to a paucity of high-quality genomes. In this study, we sequenced 5 novel Endozoicomonas strains and re-sequenced 1 known strain to improve genomic resolution. By integrating these 6 high-quality genomes with 31 qualified published genomes, our pan-genomic analysis revealed variation in genetic traits among clades. Notably, Endozoicomonas lacks quorum-sensing capabilities, suggesting resistance to quorum quenching mechanisms. It also lacks the capacity to synthesise and transport vitamin B12, indicating that it does not supply this nutrient to holobionts. Remarkably, Endozoicomonas genomes encode 92 identified giant proteins (15–65 kbp). These proteins cluster into three major groups associated with antimicrobial peptide synthesis, exotoxin production and cell adhesion. Additionally, we found that Endozoicomonas has acquired prophages from diverse sources via infection or other types of gene transfer. Notably, CRISPR-Cas sequences suggest evolutionary trajectories independent of both prophage acquisition and phylogenetic lineage, implying potential geographic influences or environmental pressures. This study provides new insights into the genomic diversity of Endozoicomonas and its genetic adaptations to diverse hosts.

Marine sediments harbour diverse microbial populations, but with increasing depth, these microbes are thought to have low activity due to depleted electron acceptors and lack of new organic matter after burial. However, physiochemical changes in environmental parameters could impact the metabolic activity of microbes in marine sediments. We performed seasonal sampling of shallow sediments to examine changes in population and abundance in relation to physiochemical changes over the year. We used amplicon sequencing, quantitative PCR and geochemistry to assess seasonal abundance of microbial populations at 3 depths (12–14, 38–40 and 48–50 cm) in shallow coastal sediments. 16S rRNA amplicon sequencing showed the sediment microbiome consists of common sediment taxa with minor seasonal variation. However, bacterial gene counts of 16S rRNA genes were highest in summer (2.50 × 10¹² genes/g of sediment) and lowest in spring (1.64 × 10¹¹ genes/g sediment). We observed differences in sediment temperature at depth across seasons (Summer 28°C–25.5°C; Winter 8.7°C–6.3°C) and correlated changes in dissolved organic matter composition that are not typically reported for this environment. We conclude deeper microbial populations in shallow sediments may experience seasonal abundance shifts resulting in a more variable subsurface community than initially presumed in the literature.