Response of Bacterial Metabolic Activity to the River Discharge in the Pearl River Estuary: Implication for CO2 Degassing Fluxes

Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria

Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be used by different heterotrophic clades. Here, we ask how a natural microbial community from the Eastern Mediterranean Sea (EMS) responds to different molecular classes of DOM (peptides, amino acids, amino sugars, disaccharides, monosaccharides, and organic acids) comprising much of the biomass of living organisms. Bulk bacterial activity increased after 24 h for all treatments relative to the control, while glucose and ATP uptake decreased or remained unchanged. Moreover, while the per-cell uptake rate of glucose and ATP decreased, that of Leucin significantly increased for amino acids, reflecting their importance as common metabolic currencies in the marine environment. Pseudoalteromonadaceae dominated the peptides treatment, while different Vibrionaceae strains became dominant in response to amino acids and amino sugars. Marinomonadaceae grew well on organic acids, and Alteromonadaseae on disaccharides. A comparison with a recent laboratory-based study reveals similar peptide preferences for Pseudoalteromonadaceae, while Alteromonadaceae, for example, grew well in the lab on many substrates but dominated in seawater samples only when disaccharides were added. We further demonstrate a potential correlation between the genetic capacity for degrading amino sugars and the dominance of specific clades in these treatments. These results highlight the diversity in DOM utilization among heterotrophic bacteria and complexities in the response of natural communities.

IMPORTANCE

A major goal of microbial ecology is to predict the dynamics of natural communities based on the identity of the organisms, their physiological traits, and their genomes. Our results show that several clades of heterotrophic bacteria each grow in response to one or more specific classes of organic matter. For some clades, but not others, growth in a complex community is similar to that of isolated strains in laboratory monoculture. Additionally, by measuring how the entire community responds to various classes of organic matter, we show that these results are ecologically relevant, and propose that some of these resources are utilized through common uptake pathways. Tracing the path between different resources to the specific microbes that utilize them, and identifying commonalities and differences between different natural communities and between them and lab cultures, is an important step toward understanding microbial community dynamics and predicting how communities will respond to perturbations.

Ecological dynamics and impacts of viruses in Chinese and global estuaries

Estuaries are important ecosystems providing irreplaceable services for humankind and, in turn, are extensively influenced by human activities and climate changes. Microbial processes, which are largely controlled by viruses, are always responsible for the ecological function and environmental problems in estuaries. However, we know little about the ecology and importance of viruses in estuarine systems. Here, we investigated viral ecological dynamics in estuarine systems on local (four largest estuaries in China in different seasons) and global scales. Viral production varied by almost 20-fold in Chinese estuaries with significant seasonality, being responsible for the removal of 1.41%-21.45% of the bacterioplankton standing stock each day, and contributed directly to the organic carbon pool by releasing an average of 3.57 µg of cellular carbon per liter per day. By compiling data from 21 estuaries across the world, we found for the first time that viral population size peaked at mid-latitude and viral production increased towards the equator in estuarine ecosystems. The results indicated the higher viral impact on microbial mortality and dissolved organic matter cycling in tropical estuaries. Our field investigation and global synthesized analysis provide compelling evidence of spatiotemporal variations in estuarine viral dynamics. The global view of viral impacts on estuarine microbial mortality offers important insight for incorporating viruses into ecological models and understanding the environmental implications of the tropicalization of temperate aquatic ecosystems under a scenario of climate warming.

Seasonal and inter-annual variability of bacterioplankton communities in the subtropical Pearl River Estuary, China

It is widely recognized that environmental factors substantially influence on the seasonal and inter-annual variability of bacterioplankton communities, yet little is known about the seasonality of bacterioplankton communities in subtropical estuaries at longer-term time scales. Here, the bacterioplankton communities from the eight major outlets of the subtropical Pearl River Estuary were investigated across 3 years (2017-2019) using full-length 16S rRNA gene sequencing. Significant seasonal and inter-annual variation was observed in bacterioplankton community compositions across the 3 years (p < 0.05). In addition, the inferred functional composition of the communities varied with seasons, although not significantly, suggesting that functional redundancy existed among communities and across seasons that could help to cope with environmental changes. Five evaluated environmental parameters (temperature, salinity, pH, total dissolved solids (TDS), total phosphorus (TP)) were significantly correlated with community composition variation, while only three environmental parameters (temperature, pH, and TDS) were correlated with variation in inferred functional composition. Moreover, community composition tracked the seasonal temperature gradients, indicating that temperature was a key environmental factor that affected bacterioplankton community's variation along with seasonal succession patterns. Gammaproteobacteria and Alphaproteobacteria were the most dominant classes in the surface waters of Pearl River Estuary, and their members exhibited divergent responses to temperature changes, while several taxa within these group could be indicators of low and high temperatures that are associated with seasonal changes. These results strengthen our understanding of bacterioplankton community variation in association with temperature-dependent seasonal changes in subtropical estuarine ecosystems.

Bio- and photo-lability of dissolved organic matter in the Pearl River (Zhujiang) estuary

We investigated the bio- and photo-lability of dissolved organic matter (DOM) from the head, mixing zone, and mouth of the Pearl River estuary. At all three sites, bio- and photo-refractory dissolved organic carbon (DOC) and biorefractory chromophoric DOM (CDOM) dominated over the corresponding bio- and photo-labile constituents, while photolabile CDOM dominated over photo-refractory CDOM. Relative to the mixing-zone and mouth waters, the headwater was enriched with bio- and photo-labile DOC and photolabile CDOM and depleted with biolabile CDOM. Biolabile DOC was richer than photolabile DOC in the headwater, while photolabile CDOM was richer than biolabile CDOM at all three sites. Pre-biotransformation inhibited, stimulated, or had little impact on DOM photodegradation, depending on site. Ultra-violet absorption coefficients are indicators of bio- and photo-refractory DOC. The relative proportions of transparent and chromophoric DOM control the turnover of biolabile DOC and the effect of pre-biotransformation on DOM photodegradation.

The impact of eutrophication towards selected bacterial process rates in tropical coastal waters

The dissolved organic nutrient conditions and bacterial process rates at two tropical coastal sites in Peninsular Malaysia (Port Klang and Port Dickson) were initially studied in 2004-2005 period and later revisited in 2010-2011. We observed that dissolved organic nitrogen (DON) increased about two- and ten-fold at Port Klang and Port Dickson, respectively and resulted in a significant change in DOC:DON ratio (t ≥ 2.077, p < 0.05). Among the bacterial processes measured, bacterial respiration (BR) was lower in the 2010-2011 period at both stations (t ≥ 3.390, p < 0.01). BR also correlated to the DOC:DON ratio (R² ≥ 0.259, p < 0.01). The increase in substrate quality enabled the bacteria to respire less in the dissolved organic matter degradation. As a result, the average bacterial growth efficiency increased slightly in the 2010-2011 period.

Environmental regulations on bacterial abundance in the South China Sea inferred from regression models

Bacteria play a critical role in carbon cycling and nutrient remineralization. To reveal potential mechanisms controlling bacterial abundance in the upper 200 m of the South China Sea (SCS), the generalized linear model (GLM), generalized additive model (GAM) and generalized boosted model (GBM) were constructed to address the relationship between bacterial abundance and environmental factors, including geographical variables, biotic variables and water chemistry. GAM and GBM were found suitable for modeling bacterial abundance in the SCS. The predictive performance of GBM was superior to GLM and GAM for bacterial distribution. In addition, bacterial abundance predicted by GBM from environmental parameters was highly consistent with the observations, indicating that GBM was robust to predict bacterial abundance from environmental parameters. Furthermore, the key environmental factors modulating the horizontal and vertical distribution of bacteria were determined based on models. Horizontally, surface bacterial abundance decreased from onshore to offshore, which was primarily regulated by salinity and chlorophyll-a. Vertically, bacterial abundance decreased with depth. Chlorophyll-a was primarily responsible for vertical variability in bacterial abundance in the upper 100 m, where temperature was higher than the optimum temperature (21 °C) for bacterial growth. In contrast, temperature was a dominant factor regulating bacterial abundance below 100 m, where temperature was below 21 °C and positively correlated with BA. Viruses and nutrients played less important roles in regulating bacterial abundance than chlorophyll-a and temperature in the SCS. Our models elucidated environmental regulations on bacterial abundance, which was helpful for us to understand bacterial carbon cycling in the SCS.

Water mass shapes the distribution patterns of planktonic ciliates (Alveolata, Ciliophora) in the subtropical Pearl River Estuary

Ciliates comprise essential components of microzooplankton in diverse marine environments. However, the extent to which environmental variables shape the distribution of planktonic ciliates in complex estuarine systems remains unclear. Here, 52 samples were collected from the Pearl River Estuary, China to reveal the influence of environmental variables on planktonic ciliate communities. Distinct community compositions of ciliates were found in three identified water masses: Pearl River diluted water mass, South China Sea surface water mass, and South China Sea bottom water mass. Significant differences in abundance, biomass, cell size, and oral diameter structure of ciliates were also detected among the three water masses. The partial Mantel test showed that water mass (as represented by water temperature and salinity) surpassed other environmental variables to be the primary factor driving the dynamics of the ciliate community. This study revealed the controlling mechanisms of planktonic ciliate communities in a subtropical, hydrographically complex estuarine ecosystem.