Biology subjects

Raut, Y.

Publications and source records attributed to Raut, Y..

6 recordsLinked to original sources

bioRxiv2026

Invariant scaling of the Species Abundance Distribution in observed and simulated marine plankton communities

Marine plankton are functionally diverse and span over five orders of magnitude in diameter, with important consequences for marine biogeochemical cycles. Marine ecosystem simulations are beginning to resolve this diversity; however, major uncertainties persist regarding the structure and function of planktonic ecosystems. Here we diagnosed plankton Species Abundance Distributions (SADs) in large-scale surveys and in a global, mechanistic plankton community simulation. The fitted slopes of the SADs vary by less than 10% across latitude, season, and biome in both observations and the simulation. Fitting parametric SADs further reveals spatial structure in the shape and functional form of the SAD aligned with established biogeographic provinces. Together, these results demonstrate a largely invariant structure of marine plankton communities that persists despite strong environmental gradients and taxonomic turnover. These findings suggest that the emergent shape and scaling of plankton SADs reflect fundamental constraints on community assembly and provide a compact quantitative diagnostic for planktonic ecosystem structure.

ecology↗

bioRxiv2026

Estimating absolute microbial abundances from metabarcoding anchored to cytometry data

Over the past decades, metabarcoding and automated cell-counting approaches have greatly advanced our understanding of marine microbial communities. Metabarcoding provides high taxonomic resolution and comprehensive community characterization, typically as relative gene abundances, whereas flow cytometry provides absolute cell abundances but lower taxonomic coverage. Here, we assess whether concurrent flow-cytometry observations can calibrate metabarcoding data to derive absolute gene abundances across four basin-scale Atlantic and Pacific Ocean transects. We first show that flow-cytometry-anchored calibration reproduces absolute abundances of Prochlorococcus and Synechococcus with performance comparable (R2 = 0.87) to internal DNA standard-based quantification. For datasets lacking internal standards, the choice of cytometric "anchor" species introduces systematic offsets in absolute abundance estimates, although spatial patterns remain robust. These offsets may reflect underestimation of cytometric counts or variation in rRNA gene copy numbers among actively dividing cells. We therefore recommend the use of multiple anchors where possible to diagnose systematic uncertainty. Applying this framework, we derive absolute gene concentrations for diverse plankton taxa from compositional metabarcoding data. For taxa with known rRNA gene copy numbers, calibration further enables estimation of absolute cell concentrations. We also resolve ecotype-level absolute abundances of Prochlorococcus along a longitudinal temperature gradient, revealing ecological patterns not apparent from compositional or cytometric data alone. Our results demonstrate that calibrated metabarcoding provides a practical quantitative bridge between molecular and cytometric observations, yielding high taxonomic resolution together with absolute gene concentrations and quantified uncertainties.

ecology↗

bioRxiv2025

A Multidomain Lens on the Temporal Dynamics of Surface Microbial Communities in the Southern Ocean (2013-2019)

Marine microorganisms are vital to biogeochemical cycles and food web dynamics, with their community structure shaped by environmental factors such as temperature, light, and salinity. While microbial dynamics in the western Antarctic Peninsula are relatively well- studied, the northwestern region remains underexplored, particularly in long-term, multidomain analyses. To fill this gap, we investigated microbial communities encompassing all three domains of life (Bacteria, Archaea, and Eukarya) in the Northwestern Antarctic Peninsula. Using the universal primer set 515Y/926R, we sequenced unfractionated seawater from ten sites over a six-year period (2013-2019). Environmental parameters, temperature and salinity, showed minimal variation across the study. However, microbial diversity and composition, especially among eukaryotic phytoplankton, displayed significant temporal changes among seasons and years. The prokaryotic community, by contrast, was relatively stable, with Gammaproteobacteria-- particularly the Nitrincolaceae family--maintaining high relative abundance throughout all sampling periods, but a few distinct ASVs. In contrast, no eukaryotic group exhibited consistently high relative abundance across sampling periods. The summer of 2016, marked by a strong El Nino event, presented the most distinct microbial community structure, underscoring the sensitivity of these communities to extreme climatic conditions. These results highlight the importance of integrated, long-term studies to better understand the dynamics, interactions, and resilience of microbial ecosystems in the rapidly changing Antarctic environment. IMPORTANCEThis study provides a unique long-term perspective on microbial community dynamics in the Northwestern Antarctic Peninsula, a region still poorly explored through a multidomain lens. By investigating the temporal variability of Bacteria, Archaea, and Eukaryotes over six years, we reveal distinct stability patterns between these groups, with phytoplankton showing the highest variability and prokaryotes remaining relatively stable. The strong response of the microbial community to the 2016 El Nino event highlights its sensitivity to extreme climate conditions, reinforcing the importance of understanding how Antarctic ecosystems will respond to future climate shifts. The consistent presence of Nitrincolaceae, a key bacterial taxon, suggests its ecological relevance in the region, while fluctuations in phytoplankton composition may impact food web dynamics. These findings emphasize the need for continued long-term monitoring to predict how microbial communities will adapt to environmental changes, which is crucial for assessing the future functioning of polar marine ecosystems.

microbiology↗

bioRxiv2025

Characterizing organisms from three domains of life with universal primers from throughout the global ocean

We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003-2020 and cover extensive latitudinal and longitudinal transects, as well as depth profiles in all major ocean basins. DNA from unfractionated (> 0.2{micro}m) seawater samples was amplified using the 515Y/926R universal three- domain rRNA gene primers, simultaneously quantifying the relative abundance of amplicon sequencing variants (ASVs) from bacteria, archaea, eukaryotic nuclear 18S, and eukaryotic plastid 16S. Thus, the ratio between taxa in one sample is directly comparable to the ratio in any other GRUMP sample, regardless of gene copy number differences. This obviates a problem in prior global studies that used size-fractionation and different rRNA gene primers for bacteria, archaea, and eukaryotes, precluding comparisons across size fractions or domains. On average, bacteria contributed 71%, eukaryotes 19%, and archaea 8% to rRNA gene abundance, though eukaryotes contributed 32% at latitudes > 40{degrees}. GRUMP is publicly available on the Simons Collaborative Marine Atlas Project (CMAP), promoting the global comparison of marine microbial dynamics.

ecology↗

bioRxiv2024

Predictable functional biogeography of marine microbial heterotrophs

Heterotrophic bacteria and archaea ( heteroprokaryotes) drive global carbon cycling, but how to quantitatively organize their functional complexity remains unclear. We generated a global-scale understanding of marine heteroprokaryotic functional biogeography by synthesizing genetic sequencing data with a mechanistic marine ecosystem model. We incorporated heteroprokaryotic diversity into the trait-based model along two axes: substrate lability and growth strategy. Using genetic sequences along three ocean transects, we compiled 21 heteroprokaryotic guilds and estimated their degree of optimization for rapid growth (copiotrophy). Data and model consistency indicated that gradients in grazing and substrate lability predominantly set biogeographical patterns, and identified deep-ocean slow copiotrophs whose ecological interactions control the surface accumulation of dissolved organic carbon.

ecology↗

bioRxiv2022

Symbiotic diazotrophic UCYN-A strains co-occurred with El Ni&ntildeo, relaxed upwelling, and varied eukaryotes over 10 years off Southern California Bight

Biological nitrogen fixation, the conversion of N2 gas into a more bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a research focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the abiotic factors that govern UCYN-As presence at the San Pedro Ocean Time-series (SPOT), its partner fidelity, and statistical interactions with non-symbiotic eukaryotes. 16S and 18S rRNA sequences were amplified by "universal primers" from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Nino event. When this "open ocean ecotype" was present, coastal upwelling ceased, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium, a potential predator, and parasitic Syndiniales. UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominate host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution patterns both locally and globally.

microbiology↗