Microbial trimethylamine metabolism in marine environments

Trimethylamine (TMA) is common in marine environments. Although the presence of this compound in the oceans has been known for a long time, unlike the mammalian gastrointestinal tract, where TMA metabolism by microorganisms has been studied intensely, many questions remain unanswered about the microbial metabolism of marine TMA. This minireview summarizes what is currently known about the sources and fate of TMA in marine environments and the different pathways and enzymes involved in TMA metabolism in marine bacteria. This review also raises several questions about microbial TMA metabolism in the marine environments and proposes potential directions for future studies

Metagenomics: Microbial diversity through a scratched lens

Since nucleic acids were first extracted directly from the environment and sequenced, metagenomics has grown to one of the most data-rich and pervasive techniques for understanding the taxonomic and functional diversity of microbial communities. In the last decade, cheaper sequencing has democratized the application of metagenomics and generated billions of reads, revealing staggering microbial diversity and functional complexity. However, cheaper sequencing has come at the cost of reduced sequence length, resulting in poor gene annotation and overestimates of bacterial richness and abundance. Recent improvements in sequencing technology are beginning to provide reads of sufficient length for accurate annotation and assembly of whole operons and beyond, that will once again enable experimental testing of gene function and re-capture the early successes of metagenomic investigations

Energy Starved Candidatus Pelagibacter Ubique Substitutes Light-Mediated ATP Production for Endogenous Carbon Respiration

Previous studies have demonstrated that Candidatus Pelagibacter ubique, a member of the SAR11 clade, constitutively expresses proteorhodopsin (PR) proteins that can function as light-dependent proton pumps. However, exposure to light did not significantly improve the growth rate or final cell densities of SAR11 isolates in a wide range of conditions. Thus, the ecophysiological role of PR in SAR11 remained unresolved. We investigated a range of cellular properties and here show that light causes dramatic changes in physiology and gene expression in Cand. P. ubique cells that are starved for carbon, but provides little or no advantage during active growth on organic carbon substrates. During logarithmic growth there was no difference in oxygen consumption by cells in light versus dark. Energy starved cells respired endogenous carbon in the dark, becoming spheres that approached the minimum predicted size for cells, and produced abundant pili. In the light, energy starved cells maintained size, ATP content, and higher substrate transport rates, and differentially expressed nearly 10% of their genome. These findings show that PR is a vital adaptation that supports Cand. P. ubique metabolism during carbon starvation, a condition that is likely to occur in the extreme conditions of ocean environments

Sources of nutrients and energy for a deep biosphere on Mars

Hydrothermal vents appear to be the tip of the subsurface biosphere in the ocean crust. The primary prducers in this biosphere are prokaryotes that tolerate a wide variety of physical and chemical conditions and are versatile in their use of inorganic compounds to drive metabolism. A synthesis of chemical and mineralogical data from Martian meteorites and measurements of the Martian surface suggest that conditions similar to those that make life possible in Earth’s oceanic crust, namely, water, carbon, nutrients, appropriate temperatures, and gradients in redox conditions, also occur within Mars. Chemolithoautotrophic microorganisms capable of living below the seafloor on Earth would probably survive some regions of the Martian subsurface

Different carboxyl-rich alicyclic molecules proxy compounds select distinct bacterioplankton for oxidation of dissolved organic matter in the mesopelagic Sargasso Sea

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Liu, S., Parsons, R., Opalk, K., Baetge, N., Giovannoni, S., Bolanos, L. M., Kujawinski, E. B., Longnecker, K., Lu, Y., Halewood, E., & Carlson, C. A. Different carboxyl-rich alicyclic molecules proxy compounds select distinct bacterioplankton for oxidation of dissolved organic matter in the mesopelagic Sargasso Sea. Limnology and Oceanography, (2020), doi:10.1002/lno.11405.Marine dissolved organic matter (DOM) varies in its recalcitrance to rapid microbial degradation. DOM of varying recalcitrance can be exported from the ocean surface to depth by subduction or convective mixing and oxidized over months to decades in deeper seawater. Carboxyl‐rich alicyclic molecules (CRAM) are characterized as a major component of recalcitrant DOM throughout the oceanic water column. The oxidation of CRAM‐like compounds may depend on specific bacterioplankton lineages with oxidative enzymes capable of catabolizing complex molecular structures like long‐chain aliphatics, cyclic alkanes, and carboxylic acids. To investigate the interaction between bacteria and CRAM‐like compounds, we conducted microbial remineralization experiments using several compounds rich in carboxyl groups and/or alicyclic rings, including deoxycholate, humic acid, lignin, and benzoic acid, as proxies for CRAM. Mesopelagic seawater (200 m) from the northwest Sargasso Sea was used as media and inoculum and incubated over 28 d. All amendments demonstrated significant DOC removal (2–11 μmol C L−1) compared to controls. Bacterioplankton abundance increased significantly in the deoxycholate and benzoic acid treatments relative to controls, with fast‐growing Spongiibacteracea, Euryarcheaota, and slow‐growing SAR11 enriched in the deoxycholate treatment and fast‐growing Alteromonas, Euryarcheaota, and Thaumarcheaota enriched in the benzoic acid treatment. In contrast, bacterioplankton grew slower in the lignin and humic acid treatments, with oligotrophic SAR202 becoming significantly enriched in the lignin treatment. Our results indicate that the character of the CRAM proxy compounds resulted in distinct bacterioplankton removal rates of DOM and affected specific lineages of bacterioplankton capable of responding.We thank Z. Landry for the inspiring idea of SAR202 catabolism of CRAM. We thank the University of California, Santa Barbara Marine Science Institute Analytical Laboratory for analyzing inorganic nutrient samples. We thank C. Johnson for her help in FISH sample processing and BATS group in supporting our project. We thank N. K. Rubin‐Saika and R. Padula for their help with amino acid sample preparation. We thank Z. Liu, J. Xue, K. Lu, and Y. Shen for their help with amino acid protocol development and validation. We thank B. Stephens for his help on microscopic image analysis. We thank M. Dasenko and the staff of the CGRB at Oregon State University for amplicon library preparation and DNA sequencing. We are grateful for the help provided by the officers and crews of the R/V Atlantic Explorer. Bermuda Institute of Ocean Sciences (BIOS) provides us tremendous support in terms of facilities and lab space. We thank Bermuda government for its allowance of our water sampling and sample export (export permit number SP160904, issued 07 October 2016 under the Fisheries Act, 1972). This project was supported by Simons Foundation International's BIOS‐SCOPE program

Exploring Vitamin B1 Cycling and Its Connections to the Microbial Community in the North Atlantic Ocean

Vitamin B1 (thiamin) is an essential coenzyme for all cells. Recent findings from experimental cell biology and genome surveys have shown that thiamin cycling by plankton is far more complex than was previously understood. Many plankton cells cannot produce thiamin (are auxotrophic) and obligately require an exogenous source of thiamin or one or more of 5 different thiamin-related compounds (TRCs). Despite this emerging evidence for the evolution among plankton of complex interactions related to thiamin, the influence of TRCs on plankton community structure and productivity are not understood. We report measurements of three dissolved TRCs 4-amino-5-aminomethyl-2-methylpyrimidine (AmMP), 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylic acid (cHET), and 4-methyl-5-thiazoleethanol (HET) that have never before been assayed in seawater. Here we characterize them alongside other TRCs that were measured previously [thiamin and 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP)], in depth profiles from a latitudinal transect in the north Atlantic in March 2018. TRC concentrations ranged from femptomolar to picomolar. Surface depletion relative to a maximum near the bottom of the euphotic zone and low concentrations at deeper depths were consistent features. Our observations suggest that when bacterial abundance and production are low, TRC concentrations approach a steady state where TRC production and consumption terms are balanced. Standing stocks of TRCs also appear to be positively correlated with bacterial production. However, near the period of peak biomass in the accumulation phase of a bloom we observed an inverse relationship between TRCs and bacterial production, coincident with an increased abundance of Flavobacteria that comparative genomics indicates could be vitamin B1 auxotrophs. While these observations suggest that the dissolved pool of TRCs is often at steady state, with TRC production and consumption balanced, our data suggests that bloom induced shifts in microbial community structure and activity may cause a decoupling between TRC production and consumption, leading to increased abundances of some populations of bacteria that are putatively vitamin B1 auxotrophs

Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening

Plant virus technology, in particular virus-induced gene silencing, is a widely used reverse- and forward-genetics tool in plant functional genomics. However the potential of virus technology to express genes to induce phenotypes or to complement mutants in order to understand the function of plant genes is not well documented. Here we exploit Potato virus X as a tool for virus-induced gene complementation (VIGC). Using VIGC in tomato, we demonstrated that ectopic viral expression of LeMADS-RIN, which encodes a MADS-box transcription factor (TF), resulted in functional complementation of the non-ripening rin mutant phenotype and caused fruits to ripen. Comparative gene expression analysis indicated that LeMADS-RIN up-regulated expression of the SBP-box (SQUAMOSA promoter binding protein-like) gene LeSPL-CNR, but down-regulated the expression of LeHB-1, an HD-Zip homeobox TF gene. Our data support the hypothesis that a transcriptional network may exist among key TFs in the modulation of fruit ripening in tomato

Identification of possible source markers in marine dissolved organic matter using ultrahigh resolution mass spectrometry

Author Posting. © Elsevier B.V., 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 73 (2009): 4384-4399, doi:10.1016/j.gca.2009.04.033.Marine dissolved organic matter (DOM) is one of the most heterogeneous and largest pools of reactive carbon on earth, rivaling in mass the carbon in atmospheric carbon dioxide. Nevertheless, the molecular-level composition of marine DOM has eluded detailed description, impeding inquiry into the specific mechanisms that add or remove compounds from the DOM pool. Here we describe the molecular-level composition of C18-extracted DOM along an east-west transect of the North Atlantic Ocean. We examine the changes in DOM composition along this transect with ultrahigh resolution mass spectrometry and multivariate statistics. We use indicator species analysis (ISA) to identify possible source markers for photochemical degradation and heterotrophic bacterial metabolism. The inclusion of ISA in statistical evaluation of DOM mass spectral data allows investigators to determine the m/z values associated with significant changes in DOM composition. With this technique, we observe indicator m/z values in estuarine water that may represent components of terrestrially-derived chromophoric DOM subject to photo-chemical degradation. We also observe a unique set of m/z values in surface seawater and show that many of these are present in pure cultures of the marine α-proteobacterium Candidatus Pelagibacter ubique when grown in natural seawater. These findings indicate that a complex balance of abiotic and biotic processes controls the molecular composition of marine DOM to produce signatures that are characteristic of different environments.The authors gratefully acknowledge the funding sources for this work: the National Science Foundation (OCE-0443217 (EBK, NVB, RDV), CAREER-OCE- 0529101(EBK)), the Gordon and Betty Moore Foundation Marine Microbiology Initiative (SJG) and WHOI startup funds (EBK)

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

<p>Abstract</p> <p>Background</p> <p>Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of '<it>Candidatus </it>Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content.</p> <p>Results</p> <p>To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of '<it>Cand</it>. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from '<it>Cand</it>. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely <it>cis</it>-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data.</p> <p>Conclusion</p> <p>This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.</p