An official website of the United States government
Managing health risks associated with human exposure to waterborne, pathogenic bacteria requires understanding the ecological dynamics of complex bacterial communities. The Hudson River Estuary (HRE) is composed of both freshwater, from tributaries and anthropogenic inputs, and marine water, due to its tidal influence. Vibrio sp., a bacterial genus that includes some pathogenic species, is highly abundant in the coastal ocean, so enters the HRE during high tides. Studies have demonstrated that the viability of particular species of Vibrio is significantly impacted by both light-induced inactivation and ambient temperature. Particle association could impact these rates because microbes attached to particles can benefit from increased nutrients, stability, and protection from UV radiation. Previous research demonstrated that natural populations of Vibrio sp. in the HRE are about 45% particle associated. In this study, we used 16S rRNA gene sequence analysis of isolates to characterize the speciation of Vibrio sp. for free-living vs. particle-associated fractions. Further, to quantify the effect of particle association, we determined light-induced loss and dark, temperature-dependent growth rates for both particle-associated, free-living and total populations of Vibrio sp. using culture-dependent enumeration. We demonstrate that particle association increases temperature-dependent growth and decreases light-induced loss of Vibrio sp.
more »
« less
This content will become publicly available on May 23, 2026
Quantitative microbial taxonomy across particle size, depth, and oxygen concentration
IntroductionMarine particles form in the ocean surface sink through the water column into the deep ocean, sequestering carbon. Microorganisms inhabit and consume carbon in these particles. The East Pacific Rise (EPR) harbors both an Oxygen Deficient Zone (ODZ) and a non-buoyant plume region formed from hydrothermal vents located on the ocean floor, allowing us to explore relationships between microbial community and particle size between a range of environments. MethodsIn this study, we quantified microbial diversity using a fractionation method that separated particles into seven fine scale fractions (0.2–1.2, 1.2–5, 5–20, 20–53, 53–180,180–500, >500 μm), and included a spike-in standard for sequencing the 16S rRNA gene. Size fractionated organic carbon into the same fractions enabled the calculation of bacterial 16S rRNA copies per μg C and per liter. ResultsThere was a large increase in the bacterial 16S rRNA copies/ug C and copies/L on particles >180 μm between the upper water column and the deep water column. Though the total concentration of organic C in particles decreased in the deep water column, the density of bacteria on large particles increased at depth. The microbial community varied statistically significantly as a function of particle size and depth. Quantitative abundance estimates found that ostensibly obligate free-living microbes, such as SAR11 and Thaumarcheota, were more abundant in the free-living fraction but also common and abundant in the particulate size fractions. Conversely, ostensibly obligate particle attached bacteria such as members of Bacteroidetes and Planctomycetes, while most abundant on particles, were also present in the free living fraction. Total bacterial abundance, and the abundance of many taxonomic groups, increased in the ODZ region, particularly in the free-living fraction. Contrastingly, in the non-buoyant plume, there were highly abundant bacteria in the 5–20 and 20–53 μm fractions but reduced bacteria present in the 53–180 and 180–500 μm fractions. ConclusionQuantitative examination of microbial communities highlights the distribution of microbial taxa unburdened by compositional effects. These data are congruent with existing models which suggest high levels of exchange between particle-attached and free-living communities.
more »
« less
- Award ID(s):
- 2421095
- PAR ID:
- 10621310
- Editor(s):
- Srivastava, Abhishek
- Publisher / Repository:
- Frontiers in Micobiology
- Date Published:
- Journal Name:
- Frontiers in Microbiology
- Volume:
- 16
- ISSN:
- 1664-302X
- Subject(s) / Keyword(s):
- marine aggregates, East Pacific Rise, oxygen deficient zone, size fractionation, organic matter, microbial communities, microbial diversity
- Format(s):
- Medium: X Other: .pdf
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005–2018), using SSU rRNA gene sequencing from two size fractions (0.2–1 and 1–80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46–93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.more » « less
-
Abstract The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatomCorethronand the bacteriaSulfitobacterwere significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellateProrocentrum texanumand prokaryotes Methanomassiliicoccales andFluviicola taffensiswere significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.more » « less
-
Raina, Jean-Baptiste (Ed.)ABSTRACT Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.more » « less
-
Abstract Marine microorganisms are drivers of biogeochemical cycles in the world’s oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.more » « less
