Limnology and Oceanography Letters最新文献

Microbial methanogenesis in marine sediments produces significant amounts of methane from various substrates; however, identifying the active pathways in situ remains challenging. While the bulk and clumped isotopic signatures of methane from different pathways have been studied in pure cultures, these are difficult to compare with complex natural settings. Previously, we linked clumped isotope signatures to the methanogenic pathway in marine sediment incubations with complete substrate conversion. Here, we investigated the temporal kinetics of microbial methane formation. Sediments were incubated with hydrogen, methanol and acetate to monitor the temporal evolution of bulk and clumped methane isotopic signatures and changes in the methanogenic community. The isotopic composition of methane exhibited a clear, substrate-specific temporal evolution, correlating with the expected methanogenic taxa enriched by each substrate. Our results contribute to understanding the kinetics and isotopic signatures of different methanogenic processes, supporting bottom-up estimations of methane emission sources from various natural environments with diverse methanogenic communities.

While the influence of salinity on microbial diversity is well documented in marine and brackish ecosystems, the impact of different dissolved inorganic ion types remains largely unexplored. In this study, we assessed how ionic composition shapes planktonic bacterial community structure in inland saline aquatic habitats, compared to the effects of salinity alone, spatial factors, and other environmental variables. We collected and analyzed 16S rRNA gene amplicon datasets from freshwater to hypersaline aquatic environments worldwide (375 samples from 130 lakes). The composition of major ions explained more variability in bacterioplankton structure than bulk salinity. Taxa contributing the most to the observed dissimilarity between communities included lineages characteristic of specific habitat types, such as Actinobacteria acI in freshwater, Halomonadaceae in saline waters, or Nitriliruptorales in soda- and soda-saline systems. Many of these indicator lineages for specific habitat types were monophyletic, further underpinning ionic composition as a crucial eco-evolutionary driver of aquatic microbial diversity.

The existence of highly productive coral reefs within oligotrophic gyres is in part due to intensive recycling of macronutrients and organic matter by microbes. Therefore, characterizing reef bacterioplankton communities is key for understanding reef metabolism and biogeochemical transformations. We performed a high-resolution survey of waters surrounding Mo'orea (French Polynesia), coupling 16S metabarcoding with biogeochemical and physical measurements. Bacterioplankton communities differed markedly among reef ecosystems on three sides of the island, and within each system distinct communities emerged in forereef, backreef and reef pass habitats. The degree of habitat differentiation varied among the island sides according to current speeds inferred from wave power. Oceanic-associated taxa were enriched in forereefs and throughout western reefs with highest wave power and lowest productivity. Reef-associated taxa were enriched in backreef and pass habitats most strongly on northern reefs with lowest wave power and highest productivity. Our results offer insight into dynamics regulating reef microbial communities.

The northern Indian Ocean is a hotspot of nitrous oxide (N₂O) emissions, with strong seasonal monsoons and interannual Indian Ocean Dipole (IOD) variability. We examine the IOD influence on N₂O seasonality using a regional ocean model covering 1981–2020, with a focus on the coastal ocean where ∆pN₂O variability is more than threefold greater than in the open ocean. Positive IOD amplifies ∆pN₂O seasonality by a factor 2 to 5 in the east and dampens it by ∼ 30% in the west. Negative IOD reverses this pattern but changes are weaker (< 10%). This east/west contrast and asymmetry between positive and negative IOD arise from changes in transport of N₂O produced in subsurface by nitrification and denitrification, and significantly modulate local N₂O emissions (−40% to +130%). Sparse N₂O observations and systematic biases in IOD phase sampling compound seasonal and interannual variability, likely leading to underestimation of N₂O seasonality and emissions in observation-based reconstructions.

Robust estimations of methane (CH₄) oxidation in marginal seas remain elusive, making CH₄ budgets particularly uncertain. Here, we investigate the CH₄ benthic source and bottom layer oxidation across the entire Baltic Sea using concentration and stable isotope (δ¹³C-CH₄) profiles along oxygen and salinity gradients. CH₄ concentrations were highest near the seafloor under low oxygen conditions. Comparison with previous local-scale studies implies increasing deep water CH₄ concentrations in the last decade. High CH₄ concentrations and δ¹³C-CH₄ values (−54.4 ± 17.7‰) in bottom waters indicate benthic sources. Oxygen, salinity, and ²²⁴Ra (benthic tracer) explained the CH₄ distribution. Methane oxidation estimated from δ¹³C-CH₄ fractionation removed 49 ± 33% of benthic-produced CH₄ before reaching the surface, leading to small water–air fluxes (10.0 ± 9.2 μmol m⁻² d⁻¹). Overall, bottom layer CH₄ oxidation was highly effective attenuating CH₄ emissions to the atmosphere.

Gelatinous zooplankton serve diverse ecological roles in shelf food webs—from grazers to predators. However, their spatial niches are poorly resolved, especially at detailed taxonomic levels, due to conventional techniques that are unable to measure distributions at fine spatial scales. Seasonal in situ imaging transects across the dynamic northern Gulf of Mexico demonstrated that taxonomic diversity of gelatinous zooplankton increases with stratification and habitat heterogeneity. Taxa displayed low spatial niche overlap (~ 10%, Schoener's D), independent of season (stratified, river-influenced, and well mixed), and even when associated with similar water mass properties. This suggests that oceanography structures the distributions of gelatinous organisms and water mass preferences, but ecological interactions among taxa generate distinct taxon-specific spatial niches. Although automated image classification algorithms currently prioritize broad taxonomic groups, detailed identifications and improved resolution of interactions (predator–prey, competition, etc.) may underlie a predictive framework for gelatinous abundances and diversity.

Blue carbon ecosystems buffer climate change via sediment carbon capture, gaining elevation and mitigating sea level rise in the process. Carbon sequestration and accretion estimates share a common methodology, whereby dry masses are converted to volume using densities. However, our analysis of 23,302 tidal marsh sediment cohorts shows that these methods overestimate carbon contribution to long-term sequestration and accretion because they incorporate both dissolved and mineral-associated organic matter. Neither dissolved nor mineral-associated organic matter contributes to sediment volume; thus, the volumetric budgets underlying estimates of organic matter contribution to predicted marsh resilience are inflated by up to 380% in the top 25-cm. This “volumeless” organic matter in surficial, uncompacted sediments is 36% greater than deeper sediments, suggesting that some carbon thought to be sequestered is lost and does not contribute to long-term storage. Combined, we demonstrate that traditional methods overestimate organic matter contributions to blue carbon stocks and accretion.

Oceans are considered significant methane sources, but the origin of methane in oxic surface seawaters remains unknown. Here, we collected seawater from the Jiulong River Estuary, Taiwan Strait, and Arctic Ocean to explore the potential for aerobic methane production. ¹³C labeling experiments revealed that methylphosphonate-based methane production widely occurs in marine ecosystems, with the methane conversion efficiency varying depending on local conditions (14.4% in the Taiwan Strait, 2.5% in the Arctic Ocean, and 0.3% in the Jiulong River Estuary). The potential for methane production from methylphosphonate could account for 3–60% of global oceanic methane emissions. Changes in the microbial composition during the incubation experiments indicated that Rhodobacterales can cleave C–P bonds to produce methane. In contrast, microbes did not directly break down C–S/N bonds. Our findings suggest that the microbial use of methylated compounds represents a potential source of methane in marine ecosystems.

When assessing the total impact of disease in a host, it is important to consider not only the disease-carrying agent but also all symbionts, as they affect and are affected by the course of disease. This concept of a pathobiome is increasingly recognized in disease ecology, but is not well-investigated in natural systems. Copepods are key organisms in marine ecosystems and host a variety of symbionts, including bacteria and eukaryotic parasites. We investigated the impact of a taxonomically uncertain yellow-hyphal parasite (YHP) on its copepod host Calanus helgolandicus with an incubation experiment, comparing survival, behavior, and microbiomes of uninfected and infected hosts. Infected hosts suffered higher mortality, and altered behavior which can increase predation risk. The microbiomes differed between infected and uninfected hosts, likely caused by a combination of direct effects of infection, and environmental effects driven by parasite-induced behavioral change. We identified several potential contributing taxa to the Calanus-YHP pathobiome using model-based ordination.

Methane (CH₄) emissions from freshwater ecosystems are significant but rarely quantified in vegetated zones. We assessed the influence of five macrophyte species that root in the sediment differing in growth form and root biomass on CH₄ emissions and sediment gas storage. Using a novel scanning method, we visualized sediment bubbles and root structures over time. Macrophyte growth form influenced diffusive as well as ebullitive emissions. Bubbles occupied a smaller volume in vegetated sediments (~ 19%) than in control treatments (~ 53%). Extensive root systems were associated with reduced sediment CH₄ accumulation, likely due to enhanced CH₄ oxidation and/or transport. Total CH₄ production was lower in vegetated (~ 54 mg CH₄ m⁻² d⁻¹) than in control treatments (103 mg CH₄ m⁻² d⁻¹), of which a substantial part was stored in sediment bubbles. Our findings highlight the importance of including changes in sediment CH₄ storage in CH₄ budgets and demonstrate how macrophyte characteristics shape CH₄ dynamics.