To kill or to piggyback: Switching of viral lysis-lysogeny strategies depending on host dynamics.

Viruses wield significant influence over microbial communities and ecosystem function in marine environments. However, the selection of viral life strategies and their impacts on microbial communities remains enigmatic. In this study, we utilized a large-scale macrocosm, established using water samples from a marine coastal region, to enable community-level investigation.

The diversity and ecological significance of microbial traits potentially involved in B biosynthesis in the global ocean.

Cobalamin (B), an essential nutrient and growth cofactor for many living organisms on Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related to B biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make-up of complex functional assemblages. By anchoring microbial traits potentially involved in B biosynthesis, we depict the biogeographic patterns of B biosynthesis genes and the taxa harboring them in the global ocean, despite the limitations of detecting de novo B synthesizers via metagenomes alone.

Decreasing O availability reduces cellular protein contents in a marine diatom.

Anthropogenic activities and climate change are exacerbating marine deoxygenation. Apart from aerobic organisms, reduced O also affects photoautotrophic organisms in the ocean. This is because without available O, these O producers cannot maintain their mitochondrial respiration, especially under dim-light or dark conditions, which may disrupt the metabolism of macromolecules including proteins.

Environmental heterogeneity and dispersal limitation simultaneously determine the spatial scaling of different microbial functional groups.

Uncovering the mechanisms driving patterns of diversity across space and through time is of critical importance in microbial community ecology. Previous studies suggest that microorganisms also follow the same spatial scaling patterns as macro-organisms. However, it remains unclear whether different microbial functional groups differ in spatial scaling and how different ecological processes may contribute to such differences.

The Transcriptional Repressor PerR Senses Sulfane Sulfur by Cysteine Persulfidation at the Structural Zn Site in sp. PCC7002.

Cyanobacteria can perform both anoxygenic and oxygenic photosynthesis, a characteristic which ensured that these organisms were crucial in the evolution of the early Earth and the biosphere. Reactive oxygen species (ROS) produced in oxygenic photosynthesis and reactive sulfur species (RSS) produced in anoxygenic photosynthesis are closely related to intracellular redox equilibrium. ROS comprise superoxide anion (O), hydrogen peroxide (HO), and hydroxyl radicals (OH).

Distinct Ecological Processes Mediate Domain-Level Differentiation in Microbial Spatial Scaling.

The spatial scaling of biodiversity, such as the taxa-area relationship (TAR) and distance-decay relationship (DDR), is a typical ecological pattern that is followed by both microbes and macrobes in natural ecosystems. Previous studies focusing on microbes mainly aimed to address whether and how different types of microbial taxa differ in spatial scaling patterns, leaving the underlying mechanisms largely untouched. In this study, the spatial scaling of different microbial domains and their associated ecological processes in an intertidal zone were comparatively investigated.

To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.

High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation.

Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly.

Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities.

Oxygen availability driven trends in DOM molecular composition and reactivity in a seasonally stratified fjord.

Ocean deoxygenation could potentially trigger substantial changes in the composition and reactivity of dissolved organic matter (DOM) pool, which plays an important role in the global carbon cycle. To evaluate links between DOM dynamics and oxygen availability, we investigated the DOM composition under varying levels of oxygen in a seasonally hypoxic fjord through a monthly time-series over two years. We used ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterize DOM on a molecular level.

Temperature Rise Increases the Bioavailability of Marine -Derived Dissolved Organic Matter.

is one group of main primary producers and plays a key role in oceanic carbon fixation and transformation. To explore how the temperature rise affects the bioavailability of -derived dissolved organic matter (SOM) and whether this effect would be altered by the involvement of heterotrophic bacteria, we compared the optical and molecular properties of the SOM of axenic sp. PCC7002 culture () to that with associated heterotrophic bacteria (B) under 15, 18, and 21C growth temperatures at exponential and decay growth phases.

An Inducible Prophage vB_MoxS-R1 Represents a Novel Lineage of Siphovirus.

Lytic and lysogenic infections are the main strategies used by viruses to interact with microbial hosts. The genetic information of prophages provides insights into the nature of phages and their potential influences on hosts. Here, the siphovirus vB_MoxS-R1 was induced from a strain isolated from an estuarine culture.

Biodegradation of Terrigenous Organic Matter in a Stratified Large-Volume Water Column: Implications of the Removal of Terrigenous Organic Matter in the Coastal Ocean.

Large amounts of terrigenous organic matter (TOM) are delivered to the ocean every year. However, removal processes of TOM in the ocean are still poorly constrained. Here, we report results from a 339-day dark incubation experiment with a unique system holding a vertically stratified freshwater-seawater column.

Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment.

Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source.

Determinism governs the succession of disturbed bacterioplankton communities in a coastal maricultural ecosystem.

Bacterioplankton community is the major engine that drives the biogeochemical cycling of various nutrient and essential elements in the coastal ecosystem. Unraveling the mechanisms governing the succession of such complex bacterioplankton communities in dynamic environment is a challenging issue in environmental science. In this study, we investigated the diversity patterns and succession mechanisms of both free-living and particle-attached bacterioplankton communities that have been exposed to low oxygen and typhoon Lekima.

Lowering O Interacts with Photoperiod to Alter Physiological Performance of the Coastal Diatom .

Exacerbating deoxygenation is extensively affecting marine organisms, with no exception for phytoplankton. To probe these effects, we comparably explored the growth, cell compositions, photosynthesis, and transcriptome of a diatom under a matrix of O levels and Light:Dark cycles at an optimal growth light. The growth rate (μ) of under a 8:16 L:D cycle was enhanced by 34% by low O but reduced by 22% by hypoxia.

Technologies and perspectives for achieving carbon neutrality.

Global development has been heavily reliant on the overexploitation of natural resources since the Industrial Revolution. With the extensive use of fossil fuels, deforestation, and other forms of land-use change, anthropogenic activities have contributed to the ever-increasing concentrations of greenhouse gases (GHGs) in the atmosphere, causing global climate change. In response to the worsening global climate change, achieving carbon neutrality by 2050 is the most pressing task on the planet.

Heterogeneous viral contribution to dissolved organic matter processing in a long-term macrocosm experiment.

Viruses saturate environments throughout the world and play key roles in microbial food webs, yet how viral activities affect dissolved organic matter (DOM) processing in natural environments remains elusive. We established a large-scale long-term macrocosm experiment to explore viral dynamics and their potential impacts on microbial mortality and DOM quantity and quality in starved and stratified ecosystems. High viral infection dynamics and the virus-induced cell lysis (6.

VBPath for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways.

Cobalamin (vitamin B12; VB) is an indispensable nutrient for all living entities in the Earth's biosphere and plays a vital role in both natural and host environments. Currently in the metagenomic era, gene families of interest are extracted and analyzed based on functional profiles by searching shotgun metagenomes against public databases. However, critical issues exist in applying public databases for specific processes such as VB biosynthesis pathways.

Correcting a major error in assessing organic carbon pollution in natural waters.

Microbial degradation of dissolved organic carbon (DOC) in aquatic environments can cause oxygen depletion, water acidification, and CO emissions. These problems are caused by labile DOC (LDOC) and not refractory DOC (RDOC) that resists degradation and is thus a carbon sink. For nearly a century, chemical oxygen demand (COD) has been widely used for assessment of organic pollution in aquatic systems.

sp. nov., isolated from coastal surface water, and reclassification of as comb. nov.

A novel Gram-stain-negative, aerobic, yellow-pigmented bacterium was isolated from seawater of Aoshan Bay, and designated as strain ASW18. Strain ASW18 was a long-rod-shaped bacterium without flagellum and lacked gliding ability. Based on 16S rRNA gene phylogeny, strain ASW18 showed the closest relationship to MCCC 1A06690, with a sequence similarity of 97.

sp. Strain PCC7002 Uses Sulfide:Quinone Oxidoreductase To Detoxify Exogenous Sulfide and To Convert Endogenous Sulfide to Cellular Sulfane Sulfur.

Eutrophication and deoxygenation possibly occur in coastal waters due to excessive nutrients from agricultural and aquacultural activities, leading to sulfide accumulation. Cyanobacteria, as photosynthetic prokaryotes, play significant roles in carbon fixation in the ocean. Although some cyanobacteria can use sulfide as the electron donor for photosynthesis under anaerobic conditions, little is known on how they interact with sulfide under aerobic conditions.