Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Limnology and Oceanography 62 (2017): 217–234, doi:10.1002/lno.10389.Picoplankton foster essential recycling of nutrients in the oligotrophic waters sustaining coral reef ecosystems. Despite this fact, there is a paucity of data on how the specific interactions between corals and planktonic bacteria and archaea (picoplankton) contribute to nutrient dynamics and reef productivity. Here, we utilized mesocosm experiments to investigate how corals and coral mucus influence picoplankton and nutrients in reef waters. Over 12 days, we tracked nutrient concentrations, picoplankton abundances and taxonomic composition of picoplankton using direct cell-counts, sequencing of SSU rRNA genes and fluorescent in situ hybridization-based abundances of dominant lineages in the presence or absence of Porites astreoides corals and with mucus additions. Our results demonstrate that when corals are present, Synechococcus, SAR11 and Rhodobacteraceae cells are preferentially removed. When corals were removed, their exudates enhanced the growth of diverse picoplankton, including SAR11 and Rhodobacteraceae. A seven-fold increase in nitrate concentration, possibly caused by nitrogen remineralization (ammonification coupled to nitrification) within the coral holobiont, may have further facilitated the growth of these taxa. In contrast, the addition of mucus resulted in rapid initial growth of total picoplankton and Rhodobacteraceae, but no measurable change in overall community structure. This study presents evidence of the multifaceted influences of corals on picoplankton, in which the coral holobiont selectively removes and promotes the growth of diverse picoplankton and remineralizes nitrogen.NSF Grant Number: OCE-1233612; NSF Oceanic Microbial Observatory Grant Number: OCE-080199

Oxygen isotopic composition of nitrate and nitrite produced by nitrifying cocultures and natural marine assemblages

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 57 (2012): 1361-1375, doi:10.4319/lo.2012.57.5.1361.The δ18O value of nitrate produced during nitrification (δ18ONO3,nit) was measured in experiments designed to mimic oceanic conditions, involving cocultures of ammonia-oxidizing bacteria or ammonia-oxidizing archaea and nitrite-oxidizing bacteria, as well as natural marine assemblages. The estimates of ranged from −1.5‰ ± 0.1‰ to +1.3‰ ± 1.4‰ at δ18O values of water (H2O) and dissolved oxygen (O2) of 0‰ and 24.2‰ vs. Vienna Standard Mean Ocean Water, respectively. Additions of 18O-enriched H2O allowed us to evaluate the effects of oxygen (O) isotope fractionation and exchange on . Kinetic isotope effects for the incorporation of O atoms were the most important factors for setting overall values relative to the substrates (O2 and H2O). These isotope effects ranged from +10‰ to +22‰ for ammonia oxidation (O2 plus H2O incorporation) and from +1‰ to +27‰ for incorporation of H2O during nitrite oxidation. values were also affected by the amount and duration of nitrite accumulation, which permitted abiotic O atom exchange between nitrite and H2O. Coculture incubations where ammonia oxidation and nitrite oxidation were tightly coupled showed low levels of nitrite accumulation and exchange (3% ± 4%). These experiments had values of −1.5‰ to +0.7‰. Field experiments had greater accumulation of nitrite and a higher amount of exchange (22% to 100%), yielding an average value of +1.9‰ ± 3.0‰. Low levels of biologically catalyzed exchange in coculture experiments may be representative of nitrification in much of the ocean where nitrite accumulation is low. Abiotic oxygen isotope exchange may be important where nitrite does accumulate, such as oceanic primary and secondary nitrite maxima.This research was funded by the National Science Foundation Chemical Oceanography grants 05-26277 and 09- 610998 to K.L.C

Targeted proteome analyses of the nitrite-oxidizing bacterium Nitrospira marina grown under atmospheric and low oxygen concentrations

Dataset: Nmarina targeted proteomeTargeted proteome analyses of the nitrite-oxidizing bacterium Nitrospira marina grown under atmospheric and low oxygen concentrations. Peptide concentrations in fmol/µg protein. Accession numbers correspond to the sequenced genome available in the JGI IMG/M repository (ID number: 2596583682). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/847378NSF Division of Ocean Sciences (NSF OCE) OCE-192451

Global proteome analyses of the nitrite-oxidizing bacterium Nitrospira marina grown under atmospheric and low oxygen concentrations

Dataset: Nmarina global proteomeGlobal proteome analyses of the nitrite-oxidizing bacterium Nitrospira marina grown under atmospheric and low oxygen concentrations. Accession numbers correspond to the sequenced genome available in the JGI IMG/M repository (ID number: 2596583682). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/847395NSF Division of Ocean Sciences (NSF OCE) OCE-192451

Nitrogen cycling in the secondary nitrite maximum of the eastern tropical North Pacific off Costa Rica

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 29 (2015): 2061–2081, doi:10.1002/2015GB005187.Nitrite is a central intermediate in the marine nitrogen cycle and represents a critical juncture where nitrogen can be reduced to the less bioavailable N2 gas or oxidized to nitrate and retained in a more bioavailable form. We present an analysis of rates of microbial nitrogen transformations in the oxygen deficient zone (ODZ) within the eastern tropical North Pacific Ocean (ETNP). We determined rates using a novel one-dimensional model using the distribution of nitrite and nitrate concentrations, along with their natural abundance nitrogen (N) and oxygen (O) isotope profiles. We predict rate profiles for nitrate reduction, nitrite reduction, and nitrite oxidation throughout the ODZ, as well as the contributions of anammox to nitrite reduction and nitrite oxidation. Nitrate reduction occurs at a maximum rate of 25 nM d−1 at the top of the ODZ, at the same depth as the maximum rate of nitrite reduction, 15 nM d−1. Nitrite oxidation occurs at maximum rates of 10 nM d−1 above the secondary nitrite maximum, but also in the secondary nitrite maximum, within the ODZ. Anammox contributes to nitrite oxidation within the ODZ but cannot account for all of it. Nitrite oxidation within the ODZ that is not through anammox is also supported by microbial gene abundance profiles. Our results suggest the presence of nitrite oxidation within the ETNP ODZ, with implications for the distribution and physiology of marine nitrite-oxidizing bacteria, and for total nitrogen loss in the largest marine ODZ.National Science Foundation. Grant Numbers OCE 05-26277, OCE 09-610998; WHOI Coastal Ocean Institute2016-06-1

Complete genome sequences of two phylogenetically distinct Nitrospina strains isolated from the Atlantic and Pacific Oceans

This paper is not subject to U.S. copyright. The definitive version was published in Bayer, B., Kellom, M., Valois, F., Waterbury, J., & Santoro, A. Complete genome sequences of two phylogenetically distinct Nitrospina strains isolated from the Atlantic and Pacific Oceans. Microbiology Resource Announcements, 11(5), (2022): e00100–e00122, https://doi.org/10.1128/mra.00100-22.The complete genome sequences of two chemoautotrophic nitrite-oxidizing bacteria of the genus Nitrospina are reported. Nitrospina gracilis strain Nb-211 was isolated from the Atlantic Ocean, and Nitrospina sp. strain Nb-3 was isolated from the Pacific Ocean. We report two highly similar ~3.07-Mbp genome sequences that differ by the presence of ferric iron chelator (siderophore) biosynthesis genes.This work was supported by a Simons Foundation Early Career Investigator Award (3435889) and a U.S. National Science Foundation award OCE-1924512 to A.E.S. B.B. was supported by the Austrian Science Fund (FWF) project number J4426-B. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under contract number DE-AC02-05CH11231. These data were generated for JGI proposal number 506203 to B.B. and A.E.S

US National BioGeoSCAPES Workshop Report

Virtual Meeting held November 10-12, 2021BioGeoSCAPES (BGS) is an international program being developed to understand controls on ocean productivity and metabolism by integrating systems biology (‘omics) and biogeochemistry (Figure 1). To ensure global input into the design of the BGS Program, countries interested in participating were tasked with holding an organizing meeting to discuss the country-specific research priorities. A United States BGS planning meeting, sponsored by the Ocean Carbon & Biogeochemistry (OCB) Project Office, was convened virtually November 10-12, 2021. The objectives of the meeting were to communicate the planning underway by international partners, engage the US community to explore possible national contributions to such a program, and build understanding, support, and momentum for US efforts towards BGS. The meeting was well-attended, with 154 participants and many fruitful discussions that are summarized in this document. Key outcomes from the meeting were the identification of additional programs and partners for BGS, a prioritization of measurements requiring intercalibration, and the development of a consensus around key considerations to be addressed in a science plan. Looking forward, the hope is that this workshop will serve as the foundation for future US and international discussions and planning for a BGS program, enabled by NSF funding for an AccelNet project (AccelNet - Implementation: Development of an International Network for the Study of Ocean Metabolism and Nutrient Cycles on a Changing Planet (BioGeoSCAPES)), beginning in 2022.This workshop was held thanks to funding to US OCB by the National Science Foundation (NSF) (OCE-1850983) and National Aeronautic and Space Administration (NASA) (NNX17AB17G). The organizers give thanks to all workshop participants for their thoughtful discussions and input during the workshop

Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes

Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant Mimiviridae, incorporating the Cafeteria roenbergensis virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (e-value < 10−5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs

Roadmap Towards Communitywide Intercalibration and Standardization of Ocean Nucleic Acids ‘Omics Measurements

In January 2020, the US Ocean Carbon & Biogeochemistry (OCB) Project Office funded the Ocean Nucleic Acids 'omics Intercalibration and Standardization workshop held at the University of North Carolina in Chapel Hill. Thirty-two participants from across the US, along with guests from Canada and France, met to develop a framework for standardization and intercalibration (S&I) of ocean nucleic acid ‘omics (na’omics) approaches (i.e., amplicon sequencing, metagenomics and metatranscriptomics). During the three-day workshop, participants discussed numerous topics, including: a) sample biomass collection and nucleic acid preservation for downstream analysis, b) extraction protocols for nucleic acids, c) addition of standard reference material to nucleic acid isolation protocols, d) isolation methods unique to RNA, e) sequence library construction, and f ) integration of bioinformatic considerations. This report provides a summary of these and other topics covered during the workshop and a series of recommendations for future S&I activities for na’omics approaches.The Ocean Nucleic Acids ‘Omics Intercalibration and Standardization Workshop was supported by grants from the Ocean Carbon & Biogeochemistry Program (OCB) – funding provided by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA) – and the Simons Foundation. This report was developed with federal support of NSF (OCE-1558412) and NASA (NNX17AB17G)

Membrane permeability selection drove the stereochemistry of life

Early in the evolution of life a proto-metabolic network was encapsulated within a membrane compartment. The permeability characteristics of the membrane determined several key functions of this network by determining which compounds could enter the compartment and which compounds could not. One key feature of known life is the utilisation of right-handed D- ribose and deoxyribose sugars and left-handed L- amino acid stereochemical isomers (enantiomers), however, it is not clear why life adopted this specific chirality. We previously demonstrated that an archaeal and an intermediate membrane mimic, bearing a mixture of bacterial and archaeal lipid characteristics (a ‘hybrid’ membrane), display increased permeability compared to bacterial-like membranes. Here, we investigate if these membranes can drive stereochemical selection on pentose sugars, hexose sugars and amino acids. Using permeability assays of homogenous unilamellar vesicles, we demonstrate that both membranes select for D- ribose and deoxyribose sugars while the hybrid membrane uniquely selects for a reduced alphabet of L- facing amino acids. This repertoire includes alanine, the plausible first L- amino acid utilised. We conclude such compartments could provide stereochemical compound selection thereby demonstrating a solution to the chirality problem during the evolution of life