Particle-associated extracellular enzyme activity and bacterial community composition across the Canadian Arctic Ocean

Particulate Organic Carbon Released during Macroalgal Growth Has Significant Carbon Sequestration Potential in the Ocean

Substantial amounts of particulate organic carbon (POC) are released during macroalgal growth; however, the fate of these POCs and their carbon sequestration effects remain unclear. Here, field investigations found that Ulva prolifera caused a significant increase of POC in seawater below the surface during a macroalgal bloom. However, laboratory simulations revealed that 77.6% of these POC was easily degraded by microorganisms in a short period of time, concurrently resulting in the production of dissolved organic carbon (DOC) from POC transformation. Over a period of 3 months, the bioavailable components of macroalgae-released POC and POC-transformed DOC were degraded, leaving 39.6% of the antibiodegradable substances composed of biorecalcitrant POC and biorecalcitrant DOC. However, although the biorecalcitrant POC was rich in humic-like components resisting biodegradation, the biorecalcitrant POC exhibited greater sensitivity to photodegradation than biorecalcitrant DOC. The photodegradation removal rate of biorecalcitrant POC (14.1%) was more than 10 times that of biorecalcitrant DOC (1.2%). Ultimately, a substantial portion (36.3%) of the POC released by growing macroalgae could potentially perform long-term carbon sequestration after conversion to recalcitrant POC and recalcitrant DOC, and these inert carbons derived from macroalgal POC have been previously ignored and should also be included in macroalgal carbon sequestration accounting.

Particles act as ‘specialty centers’ with expanded enzymatic function throughout the water column in the western North Atlantic

Heterotrophic bacteria initiate the degradation of high molecular weight organic matter by producing an array of extracellular enzymes to hydrolyze complex organic matter into sizes that can be taken up into the cell. These bacterial communities differ spatially and temporally in composition, and potentially also in their enzymatic complements. Previous research has shown that particle-associated bacteria can be considerably more active than bacteria in the surrounding bulk water, but most prior studies of particle-associated bacteria have been focused on the upper ocean - there are few measurements of enzymatic activities of particle-associated bacteria in the mesopelagic and bathypelagic ocean, although the bacterial communities in the deep are dependent upon degradation of particulate organic matter to fuel their metabolism. We used a broad suite of substrates to compare the glucosidase, peptidase, and polysaccharide hydrolase activities of particle-associated and unfiltered seawater microbial communities in epipelagic, mesopelagic, and bathypelagic waters across 11 stations in the western North Atlantic. We concurrently determined bacterial community composition of unfiltered seawater and of samples collected via gravity filtration (>3 μm). Overall, particle-associated bacterial communities showed a broader spectrum of enzyme activities compared with unfiltered seawater communities. These differences in enzymatic activities were greater at offshore than at coastal locations, and increased with increasing depth in the ocean. The greater differences in enzymatic function measured on particles with depth coincided with increasing differences in particle-associated community composition, suggesting that particles act as ‘specialty centers’ that are essential for degradation of organic matter even at bathypelagic depths.

Stochastic processes shape the aggregation of free-living and particle-attached bacterial communities in the Yangtze River Estuary, China

An estuary plays an important role in material and energy exchange between the land and sea, where complex physical, chemical, and biological processes occur. Here, we investigated the assembly processes of free-living (FL) and particle-associated (PA) bacterial communities in two seawater layers at five stations in the Yangtze River Estuary (YRE) by using 16S rRNA sequencing methods. The results indicated that Proteobacteria was the most abundant phylum in the YRE. The α-diversity of PA community was significantly higher than FL community, and analysis of similarity showed significantly different (Global R = 0.2809, p < 0.005). RDA revealed that phosphate (PO₄ ^3- ) was significantly correlated with PA bacterial community abundance (p < 0.05). An ecological null model showed that both PA and FL bacterial communities were mainly influenced by stochastic processes (PA: 100%, FL: 70%), which PA attached to nutrient particles and are less affected by environmental filtration. Dispersal limitation (50%) was the main assembly process of the PA community, while homogeneous selection (30%) and drift (30%) were important processes in the FL community assembly. The available substrate for colonization limits the transformation from FL to PA bacteria. This study would improve our understanding of FL and PA bacterial community structure and factors affecting assembly process in estuarine environments.

Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent

Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 μm) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05–0.27) of FL bacteria (defined as the size-fraction <3.0 μm) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.

Abundance and diversity of antibiotic resistance genes and bacterial communities in the western Pacific and Southern Oceans

This study investigated the abundance and diversity of antibiotic resistance genes (ARGs) and the composition of bacterial communities along a transect covering the western Pacific Ocean (36°N) to the Southern Ocean (74°S) using the Korean icebreaker R/V Araon (total cruise distance: 14,942 km). The relative abundances of ARGs and bacteria were assessed with quantitative PCR and next generation sequencing, respectively. The absolute abundance of ARGs was 3.0 × 10⁶ ± 1.6 × 10⁶ copies/mL in the western Pacific Ocean, with the highest value (7.8 × 10⁶ copies/mL) recorded at a station in the Tasman Sea (37°S). The absolute abundance of ARGs in the Southern Ocean was 1.8-fold lower than that in the western Pacific Ocean, and slightly increased (0.7-fold) toward Terra Nova Bay in Antarctica, possibly resulting from natural terrestrial sources or human activity. β-Lactam and tetracycline resistance genes were dominant in all samples (88-99%), indicating that they are likely the key ARGs in the ocean. Correlation and network analysis showed that Bdellovibrionota, Bacteroidetes, Cyanobacteria, Margulisbacteria, and Proteobacteria were positively correlated with ARGs, suggesting that these bacteria are the most likely ARG carriers. This study highlights the latitudinal profile of ARG distribution in the open ocean system and provides insights that will help in monitoring emerging pollutants on a global scale.

Suspended particles are hotspots for pathogen-related bacteria and ARGs in coastal beach waters of northern China

Marine suspended particles are unique micro-habitats for diverse microbes and also hotspots of microbially metabolic activities. However, the association of bacterial pathogens, especially those carrying antibiotic resistance genes (ARGs), with these particles remain largely unknown in coastal habitats. This study investigated the distribution of pathogen-related bacteria and ARGs in particle-associated (PA) and free-living (FL) fractions of samples collected at three coastal beaches using NextGen sequencing and qPCR. Suspended particles were found to harbor significantly higher abundances of bacteria of pathogen-related genera and ARGs than their counterparts. Functional analysis of microbial community suggested that antibiotic biosynthetic pathways were also more abundant among PA microbiome comparing to FL microbial community, which further facilitated the spread of ARGs. Additionally, 13 pathogen-related genera co-occurred with ARG in PA fraction while only 2 pathogen-related genera co-occurred with ARGs in FL fraction. Overall, our research revealed suspended particles harbored more abundant pathogen-related genera and ARGs comparing with surrounding waters. Thus, suspended particles are hotspots for pathogen-related genera and ARGs and may pose a greater threat to human health in coastal beach.

Temporal changes in water temperature and salinity drive the formation of a reversible plastic-specific microbial community

Plastic is a ubiquitous pollutant in the marine environment. Here, we investigated how temporal changes in environmental factors affect the microbial communities formed on plastic (polyethylene terephthalate; PET) versus a ceramic substrate. In situ mesocosms (N = 90 replicates) were deployed at the sediment-water interface of a coastal lagoon and sampled every 4 weeks for 424 days. Sequencing data (16S rRNA) was parsed based on variation in temperature with the exposure starting in fall 2016 and remaining in situ through the next four seasons (winter, spring, summer and fall 2017). PET biofilms were distinct during the summer when salinity and temperature were highest. In particular, a significant shift in the relative abundance of Ignavibacteriales and Cytophagales was observed during the summer, but PET and ceramic communities were again indistinguishable the following fall. Water temperature, salinity and pH were significant drivers of PET biofilm diversity as well as the relative abundance of plastic-discriminant taxa. This study illustrates the temporal and successional dynamics of PET biofilms and clearly demonstrates that increased water temperature, salinity, pH and exposure length play a role in the formation of a plastic-specific microbial community, but this specificity can be lost with a change in environmental conditions.

Seasonal variations in extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water

Seasonal changes of microbial abundance and associated extracellular enzymatic activity in marine snow and in seawater were studied in the northern Adriatic during a three-year period. Marine snow was present during the entire period of investigation, although in higher concentrations during summer than during winter. Microorganisms densely colonized marine snow and aggregate-associated enzymatic activity was substantially higher (up to 105 times) than in seawater. Alkaline phosphatase activity (APA) and aminopeptidase activity in marine snow showed seasonal variations with higher values in late spring-summer than in autumn-winter, probably in response to changes in the quantity and quality of organic matter. The highest cell-specific bacterial activity was found for phosphatase, followed by peptidase, and the lowest was for glucosidases. Differential hydrolysis of marine snow-derived organic matter points to the well-known phosphorus limitation of the northern Adriatic and indicates preferential utilization of phosphorus- and nitrogen-rich organic compounds by microbes, while hydrolysis of polysaccharides seemed to be less important. In oligotrophic conditions during summer, organic matter released from marine snow might represent a significant source of substrate for free-living bacteria in seawater. For the first time microorganisms producing APA in marine snow were identified, revealing that dense populations of bacteria expressed APA, while cyanobacteria did not. Cyanobacteria proliferating in marine snow could benefit from phosphorus release by bacteria and nanoflagellates.

Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment

Plastic is incredibly abundant in marine environments but little is known about its effects on benthic microbiota and biogeochemical cycling. This study reports the shotgun metagenomic sequencing of biofilms fouling plastic and bioplastic microcosms staged at the sediment–water interface of a coastal lagoon. Community composition analysis revealed that plastic biofilms were indistinguishable in comparison to a ceramic biofilm control. By contrast, bioplastic biofilms were distinct and dominated by sulfate-reducing microorganisms (SRM). Analysis of bioplastic gene pools revealed the enrichment of esterases, depolymerases, adenylyl sulfate reductases (aprBA), and dissimilatory sulfite reductases (dsrAB). The nearly 20-fold enrichment of a phylogenetically diverse polyhydroxybutyrate (PHB) depolymerase suggests this gene was distributed across a mixed microbial assemblage. The metagenomic reconstruction of genomes identified novel species of Desulfovibrio, Desulfobacteraceae, and Desulfobulbaceae among the abundant SRM, and these genomes contained genes integral to both bioplastic degradation and sulfate reduction. Findings indicate that bioplastic promoted a rapid and significant shift in benthic microbial diversity and gene pools, selecting for microbes that participate in bioplastic degradation and sulfate reduction. If plastic pollution is traded for bioplastic pollution and sedimentary inputs are large, the microbial response could unintentionally affect benthic biogeochemical activities through the stimulation of sulfate reducers.

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

Bacterial production (BP), respiration (BR) and growth efficiency (BGE) were simultaneously determined along an environmental gradient in the Pearl River Estuary (PRE) in the wet season (May 2015) and the dry season (January 2016), in order to examine bacterial responses to the riverine dissolved organic carbon (DOC) in the PRE. The Pearl River discharge delivered labile dissolved organic matters (DOM) with low DOC:DON ratio, resulting in a clear gradient in DOC concentrations and DOC:DON ratios. BP (3.93-144 μg C L^-1 d^-1) was more variable than BR (64.6-567 μg C L^-1 d^-1) in terms of the percentage, along an environmental gradient in the PRE. In response to riverine DOC input, BP and the cell-specific BP increased; in contrast, the cell-specific bacterial respiration declined, likely because labile riverine DOC mitigated energetic cost for cell maintenance. Consequently, an increase in bacterial respiration was less than expected. Our findings implied that the input of highly bioavailable riverine DOC altered the carbon portioning between anabolic and catabolic pathways, consequently decreasing the fraction of DOC that bacterioplankton utilized for bacterial respiration. This might be one of the underlying mechanisms for the low CO₂ degassing in the PRE receiving large amounts of sewage DOC.

Role of organic components in regulating denitrification in the coastal water of Daya Bay, southern China

Both dissolved and particulate organic materials have been proposed to be important factors in regulating heterotrophic denitrification in various aquatic environments. However, the specific pathways and mechanisms remain elusive. In this study, water column samples were collected from Daya Bay, southern China, to examine the relationships between potential denitrification and different organic components in the water column. Bulk dissolved organic carbon (DOC) was categorized into three major components including terrigenous fluorescent (tFDOC), autochthonous fluorescent (bFDOC) and non-fluorescent (nFDOC) fractions, while the bulk particulate organic carbon (POC) was divided into terrigenous (tPOC) and autochthonous (bPOC) fractions based on an isotope mixing model. Potential denitrification derived from in situ incubation experiments under anoxic conditions was evident (ranging from 6 to 107 nmol N2 per L per h) and varied markedly among stations. When normalized to nitrate concentration, the denitrification rate (NDR) followed a positive trend with either the concentration or proportion of tFDOC, and a negative trend with the proportion of nFDOC, suggesting tFDOC was potentially favorable while nFDOC was unfavorable for denitrifying degradation. In comparison, the NDR showed a significant positive correlation with the proportion of bPOC in the bulk POC (p = 0.01), with a predictive power of >70%, indicating that the composition of POC has a substantial impact on potential denitrification. Furthermore, if both bPOC and suspended particulate matter (SPM) were considered as variables concurrently, the variability of NDR can be better predicted with a predictive power as high as 80%. Therefore, denitrifiers may preferentially utilize fresher and labile autochthonous POC instead of DOC especially in coastal waters where particles/colloids are abundant. Our results thus provide new insights for a better understanding of denitrification mechanisms in water columns and the importance of both suspended particles and POC components in regulating denitrification, especially in turbid and productive coastal environments.

Secretion of DNases by Marine Bacteria: A Culture Based and Bioinformatics Approach

The vast majority of bacteria present in the natural environment are present in the form of aggregates and/or biofilms. Microbial aggregates are ubiquitous in the marine environment and are inhabited by diverse microbial communities which often express intense extracellular enzymatic activities. However, the secretion of an important group of enzymes, DNases, by bacteria from marine aggregates has not been studied, despite the importance of these aggregates in biogeochemical cycling of nutrients in the oceans. In this work, we therefore, employed both culture-based and bioinformatics approaches to understand the diversity of bacterial DNases in marine bacterioplankton. We found that 34% of 345 strains of attached and non-attached marine bacteria showed extracellular DNase activity. Most of these isolates belong to Proteobacteria (53%) and Firmicutes (34%). Secretion of DNases by bacteria isolated from marine gel particles (MGP) is reported here for the first time. Then, to further understand the wider diversity of the potential to produce DNases, sequences were compared using 2316 whole genome and 42 metagenome datasets. Thirty-nine different taxonomic groups corresponding to 10 bacterial phyla were found to encode genes responsible for DNase secretion. This study highlights the unexpected and widespread presence of DNase secretion in bacteria in general and in MGP more specifically. This has important implications for understanding the dynamics and fate of marine microbial aggregates in the oceans.

Contrasting Network Features between Free-Living and Particle-Attached Bacterial Communities in Taihu Lake

Free-living (FL) and particle-attached (PA) bacterial communities play critical roles in nutrient cycles, metabolite production, and as a food source in aquatic systems, and while their community composition, diversity, and functions have been well studied, we know little about their community interactions, co-occurrence patterns, and niche occupancy. In the present study, 13 sites in Taihu Lake were selected to study the differences of co-occurrence patterns and niches occupied between the FL and PA bacterial communities using correlation-based network analysis. The results show that both FL and PA bacterial community networks were non-random and significant differences of the network indexes (average path length, clustering coefficient, modularity) were found between the two groups. Furthermore, the PA bacterial community network consisted of more correlations between fewer OTUs, as well as higher average degree, making it more complex. The results of observed (O) to random (R) ratios of intra- or inter-phyla connections indicate more relationships such as cross-feeding, syntrophic, mutualistic, or competitive relationships in the PA bacterial community network. We also found that four OTUs (OTU00074, OTU00755, OTU00079, and OTU00454), which all had important influences on the nutrients cyclings, played different roles in the two networks as connectors or module hubs. Analysis of the relationships between the module eigengenes and environmental variables demonstrated that bacterial groups of the two networks favored quite different environmental conditions. These findings further confirmed the different ecological functions and niches occupied by the FL and PA bacterial communities in the aquatic ecosystem.

Effects of particles on potential denitrification in the coastal waters of the Beibu Gulf in China

Although the influence of suspended particulate matter (SPM) on denitrifying activity has been identified in river waters recently through metabolic incubations and community gene analysis, the regulations of SPM to denitrification in marine systems are still poorly understood. In the present study, the effects of suspended particle properties (including concentration, composition and size) on potential denitrification were explored in the coastal Beibu Gulf water columns based on a series of ¹⁵N-labeled incubations under artificial anaerobic condition. A gradient of oxygen (O₂) concentrations was also manipulated in the incubated seawaters to test the sensitivity of denitrification to O₂ exposure. According to our experiments, potential denitrification was the dominant pathway for N₂ production with major contribution (>60%) recovered from the particle-associated (PA) fraction. The Highest rate occurred in the benthic nepheloid layer, where high particle content induced by sediment resuspension were observed, suggesting that resuspended particles may act as a hot spot for marine nitrogen (N) loss. Both content and lability of particulate organic carbon (POC) were tightly related to the denitrification rates, with denitrification enhanced by autochthonous POC fractions more significantly. The PA denitrification was higher on small particles (1.2-10μm) compared to the large ones (>10μm), probably due to larger specific surface area and higher specific POC content in small particles. O₂ suppressed denitrifying activity for both bulk water samples and PA fractions. Although in situ denitrifying activity should be minor or neglected because of high-O₂ inhibition, the novel findings of particle effects on anaerobic denitrification can still be applied to hypoxic marine environments. Our research also implies that resuspended particles from sediment may act as a hot spot for N loss, and therefore to be a first step toward future studies in high particle loaded marine regimes.

An alternative polysaccharide uptake mechanism of marine bacteria

Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered-using super-resolution structured illumination microscopy-that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS). Fluorescence in situ hybridisation identified these organisms as members of the bacterial phyla Bacteroidetes and Planctomycetes and the gammaproteobacterial genus Catenovulum. Simultaneous membrane staining with nile red indicated that the FLA-PS labelling occurred in the cell but not in the cytoplasm. The dynamics of FLA-PS staining was further investigated in pure culture experiments using Gramella forsetii, a marine member of Bacteroidetes. The staining patterns observed in environmental samples and pure culture tests are consistent with a 'selfish' uptake mechanisms of larger oligosaccharides (>600 Da), as demonstrated for gut Bacteroidetes. Ecologically, this alternative polysaccharide uptake mechanism secures substantial quantities of substrate in the periplasmic space, where further processing can occur without diffusive loss. Such a mechanism challenges the paradigm that hydrolysis of HMW substrates inevitably yields low-molecular-weight fragments that are available to the surrounding community and demonstrates the importance of an alternative mechanism of polysaccharide uptake in marine bacteria.