Limnology and Oceanography最新文献

While metagenomics can provide insight into microbial community metabolic potential, understanding factors that influence gene abundance is necessary to maximize the information gained from this analysis. Gene abundances are influenced by chemical or physical conditions along with other factors, such as copy number variation between taxa, methodological biases, or issues associated with identification and classification. Here, we identify major drivers of spatiotemporal shifts in microbial gene relative abundance from multiple months, sites, and depths within Chesapeake Bay in 2017 using shotgun metagenomics. We compared changes in relative abundance of key genes for bacterial photosynthesis, nitrogen, and sulfur metabolism with each other and measured environmental variables. Major drivers of differences in key metabolic gene abundances are associated with environmental variables that largely change with depth and season (e.g., temperature, oxygen, phosphate). For sulfur oxidation, bacterial photosynthesis, and denitrification, genes within each process are generally significantly correlated with each other and with several environmental variables. For other processes, such as nitrification, nitrogen fixation, and dissimilatory nitrate reduction to ammonium, genes that encode enzymes within the same pathway are not well correlated. The lack of correlation typically results from differences in identified taxa carrying these genes, suggesting modular pathway structure, methodological errors, or discrepancies in gene copy number between taxonomic groups. To be suitable indicators of biogeochemical processes for models, genes or pathways should be strongly correlated with environmental variables and specific to and inclusive of all taxa mediating the associated process.

Prokaryotic communities play a dominant role in driving biogeochemical cycling in marine ecosystems. How short-term temperature increase impacts prokaryotes in subtropical coastal waters is still largely unknown. Here, 14 field experiments were conducted to investigate the response of prokaryotes in subtropical coastal waters to temperature increases of 3°C and 6°C, encompassing a range of ambient temperatures from 17°C to 31°C. We found that responses of prokaryotic growth, grazing pressure, community, and transcriptomes to increased temperatures were largely affected by ambient temperatures. Increased temperatures enhanced the growth rate and grazing pressure of heterotrophic prokaryotes when ambient temperatures were below 26–28°C. The increased temperatures had greater negative effects on the grazing rate compared to the growth rate; therefore, the abundance of heterotrophic prokaryotes generally increased after temperature increase across all temperature regimes. Metatranscriptomics analysis showed that at an ambient temperature of 30°C, genes involved in the adenosine triphosphate synthase were significantly downregulated by the increased temperature. This could be a major factor contributing to the decreased prokaryotic growth rate. In comparison, autotrophic prokaryotes (Synechococcus) exhibited better performance in response to elevated temperatures, thriving up to 35°C, beyond which their growth rate experienced a dramatic decline. When exposing to extremely high temperatures, genes involved in photosynthesis significantly decreased. These findings highlight the differential ecological impacts of temperature increase on prokaryotic communities, varying across different ambient temperatures and taxa in subtropical coastal waters.

Dissolved oxygen (DO) in the bottom layer is essential for benthic organisms, and its temporal variations are widely concerned. However, previous studies have primarily focused on the long-term variations of bottom DO, leaving its high-frequency (HF) dynamics inadequately understood. This study addresses this gap by utilizing two seafloor monitoring systems that provide 3-year-long HF records in a typical temperate shelf sea, the Bohai Sea, China. During the stratified period each year, bottom DO exhibits notable HF fluctuations superimposed on its seasonal cycle. These HF signals originate from tide-induced vertical mixing, showing peaks at various tidal frequencies. Notably, significant shallow-water tidal signals are observed in bottom DO due to the frequency doubling of semi-diurnal and diurnal tidal currents. Moreover, bottom DO demonstrates strongly asymmetric responses to tidal mixing on HF time scales. To be specific, the bottom DO increases with the intensity of tidal mixing, with this process being exceptionally rapid under conditions of weak tidal mixing. The underlying cause of this asymmetry is the markedly stronger vertical DO gradient near the seabed due to sediment oxygen demand. A process-oriented biological model successfully reproduced observational features, further supporting our theoretical inference. These findings highlight the joint role of tidal mixing and sediment oxygen demand in modulating the HF dynamics of bottom DO in temperate shelf seas, underscoring their significance for the refined prediction of bottom DO in the future.