Biology subjects

Sidhu, C.

Publications and source records attributed to Sidhu, C..

4 recordsLinked to original sources

bioRxiv2024

Resource partitioning in organosulfonate utilization by free-living heterotrophic bacteria during a North Sea microalgal bloom

Blooming microalgae (phytoplankton) release diverse organic molecules that fuel the marine pools of dissolved and particulate organic matter. A highly specialized community of heterotrophic bacteria rapidly remineralizes substantial parts of this organic matter in the sun-lit upper ocean. In particular, microalgae produce large quantities of various organosulfur compounds that can serve as carbon and sulfur sources for bacteria. Here, we report on the analyses of a time series of previously generated 30 long-read metagenomes, 30 corresponding deeply sequenced short-read metatranscriptomes and 15 metaproteomes from 0.2-3 {micro}m size fractions that we sampled in 2020 during a biphasic phytoplankton bloom in the German Bight (Southern North Sea). We analyzed the assembled contigs as well as 70 bacterial metagenome-assembled genomes that recruited the highest transcript numbers with respect to the utilization of methyl sulfur compounds (dimethylsulfoniopropionate (DMSP), dimethyl sulfide (DMS), dimethyl sulfone (DMSO2)), C3-sulfonates (2,3-dihydroxypropane-1-sulfonate (DHPS), 3-sulfolactate, 3-sulfopyruvate) and 2-aminoethanesulfonic acid (taurine). We observed a pronounced resource partitioning among bacterial clades that utilize distinct organosulfur compounds, which may explain successions of these clades during the studied bloom. Alphaproteobacteria were the most active and degraded a variety of organosulfonates via various metabolic routes. However, we also found previously underreported roles of members of the Bacteroidota and Gammaproteobacteria as efficient degraders of DMSP, DMS, and DMSO2. One striking observation was a strong preference for DMSP cleavage in Bacteroidota as opposed to DMSP demethylation in Alphaproteobacteria and indications for a particular proficiency for taurine utilization in Ilumatobacter_A and Acidimicrobiia. ImportanceSulfur-containing low-molecular-weight algal metabolites play an important role in overall marine carbon and sulfur fluxes. This study highlights that such compounds may play a crucial role in governing the succession of distinct bacterioplankton clades in response to phytoplankton blooms in coastal shelf areas of the temperate zone, such as the German Bight of the North Sea. While Alphaproteobacteria are the most versatile and competitive degraders of dissolved organosulfur compounds during such blooms, this study repositions clades previously thought to play only a more limited role in dissolved organosulfur metabolism in situ, such as Gammaproteobacteria, Bacteroidota, and Acidimicrobiia, as crucial contributors to the remineralization of organosulfur compounds in the upper ocean. This study also highlights the high level of interconnectedness of bacterial carbon and sulfur cycling during phytoplankton blooms.

ecology↗

bioRxiv2024

Polyelectrolyte mannan from diatoms reshapes sunlit ocean microbiome

Diatoms are a keystone phylum in Earths ecosystems, specializing in oxygen production and carbohydrate fixation that fuels global food webs. Diatoms host a microbiome, but how they preferentially collect bacteria with complementary traits remains unknown. Here we show that diatoms exude a C6-sulfated -1,3-mannan that serves as a selective carbon source for adapted bacteria. Its structure was resolved by NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses revealed that specialized Bacteroidota employ a four-enzyme pathway to metabolize this mannan. Metagenomic and transcriptomic data indicate that the mannan globally selects for bacteria carrying these enzymes and associated traits. Because the mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements from alternative sources, reinforcing metabolic interdependence. We propose that diatoms use sulfated mannans to attract beneficial partners and exclude competitors, thereby engineering a microbiome that enhances their productivity and underpins carbon cycling. Significance statementEukaryotes host microbial partners that shape their health, yet how they selectively assemble beneficial microbes remains unclear. Using diatom microalgae as a model, we show they exude a sulfated mannan that nourishes highly adapted bacteria tracking them across the global ocean. Our findings suggest that single-celled eukaryotes can "domesticate" prokaryotes--analogous to how humans have domesticated animals--albeit on a microscopic scale. Dominating much of Earths aquatic surface, diatoms drive [~]20% of global photosynthesis. We propose that sulfated mannan contributes to this success by helping diatoms shape microbial partnerships that underpin planetary energy balance and atmospheric chemistry.

ecology↗

bioRxiv2022

Grazers affect the composition of dissolved storage glycans and thereby bacterioplankton composition during a biphasic North Sea spring algae bloom

Blooms of marine microalgae play a pivotal role in global carbon cycling. Such blooms entail successive blooms of specialized clades of planktonic bacteria that remineralize algal biomass. We investigated the bacterioplankton response to a bloom in the German Bight in spring 2020. Metagenome sequencing at 30 time-points allowed reconstruction of 251 metagenome-assembled genomes (MAGs), 245 representing as yet uncultured species, while corresponding metatranscriptome sequencing highlighted 50 particularly active MAGs. Together with algae, copepod, protist and bacteria diversity and abundance data in combination with physico-chemical data and antibody-based saccharide measurements, we demonstrate (i) how dissolved primary photoassimilated algal and secondary bacterial storage glycans shape the bacterioplankton community composition, and (ii) how grazing on higher trophic levels determines the release of these abundant glycans. We thus elucidate principles governing how bacterioplankton clades respond to algal blooms and collectively remineralize gigatons of carbon annually on a global scale.

ecology↗

bioRxiv2022

Transcriptomics sheds light on N2-fixation strategies employed by a thermophilic member of the Methanococcales

Some marine thermophilic methanogens are able to perform energy-consuming nitrogen fixation despite deriving only little energy from hydrogenotrophic methanogenesis. We studied this process in Methanothermococcus thermolithotrophicus DSM 2095, a methanogenic archaeon of the order Methanococcales, that contributes to the nitrogen pool in some marine environments. We successfully grew this archaeon under diazotrophic conditions in both batch and fermenter cultures, reaching the highest cell density reported so far. Diazotrophic growth depended strictly on molybdenum and, in contrast to other diazotrophs, was not inhibited by tungstate or vanadate. This suggests an elaborate control of metal uptake and a specific metal recognition system for the insertion into the nitrogenase cofactor. Differential transcriptomics of M. thermolithotrophicus grown under diazotrophic conditions with ammonium-fed cultures as controls revealed upregulation of the nitrogenase machinery including chaperones, regulators, and molybdate-importers, as well as simultaneous upregulation of an ammonium-transporter and a putative pathway for nitrate/nitrite utilization. The organism thus employs multiple synergistic strategies for uptake of nitrogen nutrients during the early exponential growth phase without altering transcription levels for genes involved in methanogenesis. As a counterpart, genes coding for transcription and translation processes were downregulated, highlighting the maintenance of an intricate metabolic balance to deal with energy constraints and nutrient limitations imposed by diazotrophy. This switch in the metabolic balance included unexpected processes, such as upregulation of the CRISPR-Cas system, probably caused by drastic changes in transcription levels of putative mobile and virus-like elements. ImportanceThe thermophilic anaerobic archaeon, M. thermolithotrophicus, is a particularly suitable model organism to study the coupling of methanogenesis to diazotrophy. Likewise, its capability to simultaneously reduce N2/CO2 into NH3/CH4 with H2 makes it a viable target for biofuel production. We optimized M. thermolithotrophicus cultivation, resulting in considerably higher cell yields and enabling the successful establishment of N2-fixing bioreactors. Improved understanding of the N2-fixation process would provide novel insights into metabolic adaptations that allow this energy-limited extremophile to thrive under diazotrophy, for instance by investigating its physiology and uncharacterized nitrogenase. We demonstrate that diazotrophic growth of M. thermolithotrophicus is exclusively dependent on molybdenum, and complementary transcriptomics corroborated the expression of the molybdenum nitrogenase system. Further analyses of differentially expressed genes during diazotrophy across three cultivation time points revealed insights into the response to nitrogen limitation and the coordination of core metabolic processes.

microbiology↗