scholarly journals efam: an expanded, metaproteome-supported HMM profile database of viral protein families

2021 ◽  
Author(s):  
Ahmed A Zayed ◽  
Dominik Lücking ◽  
Mohamed Mohssen ◽  
Dylan Cronin ◽  
Ben Bolduc ◽  
...  
Keyword(s):  
Viral Protein ◽  
Global Ocean ◽  
Supplementary Information ◽  
Protein Families ◽  
Marine Habitats ◽  
Elemental Cycling ◽  
Protein Functions ◽  
Minimum Zone ◽  
Viral Sequences ◽  
Oxygen Minimum

Abstract Motivation Viruses infect, reprogram, and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Results Here we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240,311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from “conservative” to “eXtremely Conservative” resulted in 37,841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem. Availability The resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families

2021 ◽  
Author(s):  
Joan Carles Pons ◽  
David Paez-Espino ◽  
Gabriel Riera ◽  
Natalia Ivanova ◽  
Nikos C Kyrpides ◽  
...  
Keyword(s):  
Viral Protein ◽  
Confidence Score ◽  
Taxonomic Classification ◽  
Global Ocean ◽  
Supplementary Information ◽  
Protein Families ◽  
Taxonomic Assignment ◽  
Genus Level ◽  
Key Steps ◽  
Viral Sequences

Abstract Motivation Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets. Results In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified. Availability and implementation The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Metabolic preference of nitrate over oxygen as an electron acceptor in foraminifera from the Peruvian oxygen minimum zone

2019 ◽  
Vol 116 (8) ◽  
pp. 2860-2865 ◽  
Author(s):  
Nicolaas Glock ◽  
Alexandra-Sophie Roy ◽  
Dennis Romero ◽  
Tanita Wein ◽  
Julia Weissenbach ◽  
...  
Keyword(s):  
Cell Volume ◽  
Electron Acceptor ◽  
Oxygen Minimum Zone ◽  
Diverse Range ◽  
Mean Cell Volume ◽  
Respiration Rates ◽  
Marine Habitats ◽  
Biogeochemical Models ◽  
Minimum Zone ◽  
Oxygen Minimum

Benthic foraminifera populate a diverse range of marine habitats. Their ability to use alternative electron acceptors—nitrate (NO3−) or oxygen (O2)—makes them important mediators of benthic nitrogen cycling. Nevertheless, the metabolic scaling of the two alternative respiration pathways and the environmental determinants of foraminiferal denitrification rates are yet unknown. We measured denitrification and O2respiration rates for 10 benthic foraminifer species sampled in the Peruvian oxygen minimum zone (OMZ). Denitrification and O2respiration rates significantly scale sublinearly with the cell volume. The scaling is lower for O2respiration than for denitrification, indicating that NO3−metabolism during denitrification is more efficient than O2metabolism during aerobic respiration in foraminifera from the Peruvian OMZ. The negative correlation of the O2respiration rate with the surface/volume ratio is steeper than for the denitrification rate. This is likely explained by the presence of an intracellular NO3−storage in denitrifying foraminifera. Furthermore, we observe an increasing mean cell volume of the Peruvian foraminifera, under higher NO3−availability. This suggests that the cell size of denitrifying foraminifera is not limited by O2but rather by NO3−availability. Based on our findings, we develop a mathematical formulation of foraminiferal cell volume as a predictor of respiration and denitrification rates, which can further constrain foraminiferal biogeochemical cycling in biogeochemical models. Our findings show that NO3−is the preferred electron acceptor in foraminifera from the OMZ, where the foraminiferal contribution to denitrification is governed by the ratio between NO3−and O2.

scholarly journals Following the N<sub>2</sub>O consumption in the oxygen minimum zone of the eastern South Pacific

2012 ◽  
Vol 9 (8) ◽  
pp. 3205-3212 ◽  
Author(s):  
M. Cornejo ◽  
L. Farías
Keyword(s):  
Primary Productivity ◽  
High Reliability ◽  
South Pacific ◽  
Global Ocean ◽  
Field Observations ◽  
N2o Production ◽  
Oxygen Minimum Zones ◽  
Minimum Zone ◽  
Existing Data ◽  
Oxygen Minimum

Abstract. Oxygen minimum zones (OMZs), such as those found in the eastern South Pacific (ESP), are the most important N2O sources in the global ocean relative to their volume. N2O production is related to low O2 concentrations and high primary productivity. However, when O2 is sufficiently low, canonical denitrification takes place and N2O consumption can be expected. N2O distribution in the ESP was analyzed over a wide latitudinal and longitudinal range (from 5° to 30° S and from 71–76° to ~ 84° W) based on ~ 890 N2O measurements. Intense N2O consumption, driving undersaturations as low as 40%, was always associated with secondary NO2– accumulation (SNM), a good indicator of suboxic/anoxic O2 levels. First, we explore relationships between ΔN2O and O2 based on existing data of denitrifying bacteria cultures and field observations. Given the uncertainties in the O2 measurements, a second relationship between ΔN2O and NO2– (> 0.75 μM) was established for suboxic waters (O2 < 8 μM). We reproduced the apparent N2O production (ΔN2O) along the OMZ in ESP with high reliability (r2 = 0.73 p = 0.01). Our results will contribute to the quantification of the N2O that is recycled in O2 deficient waters, and improve the prediction of N2O behavior under future scenarios of OMZ expansion and intensification.

scholarly journals Ammonium excretion and oxygen respiration of tropical copepods and euphausiids exposed to oxygen minimum zone conditions

2015 ◽  
Vol 12 (20) ◽  
pp. 17329-17366 ◽  
Author(s):  
R. Kiko ◽  
H. Hauss ◽  
F. Buchholz ◽  
F. Melzner
Keyword(s):  
Partial Pressure ◽  
Oxygen Minimum Zone ◽  
Global Ocean ◽  
Carbon Dioxide Partial Pressure ◽  
Ammonium Excretion ◽  
Implicit Assumption ◽  
Calanoid Copepods ◽  
Near Surface ◽  
Minimum Zone ◽  
Oxygen Minimum

Abstract. Calanoid copepods and euphausiids are key components of marine zooplankton communities worldwide. Most euphausiids and several copepod species perform diel vertical migrations (DVMs) that contribute to the export of particulate and dissolved matter to midwater depths. In vast areas of the global ocean, and in particular in the eastern tropical Atlantic and Pacific, the daytime distribution depth of many migrating organisms corresponds to the core of the oxygen minimum zone (OMZ). At depth, the animals experience reduced temperature and oxygen partial pressure (pO2) and an increased carbon dioxide partial pressure (pCO2) compared to their near-surface nighttime habitat. Although it is well known that low oxygen levels can inhibit respiratory activity, the respiration response of tropical copepods and euphausiids to relevant pCO2, pO2 and temperature conditions remains poorly parameterized. Further, the regulation of ammonium excretion at OMZ conditions is generally not well understood. It was recently estimated that DVM-mediated ammonium supply considerably fuels bacterial anaerobic ammonium oxidation – a major loss process for fixed nitrogen in the ocean. These estimates were based on the implicit assumption that hypoxia or anoxia in combination with hypercapnia (elevated pCO2) does not result in a downregulation of ammonium excretion. Here we show that exposure to OMZ conditions can result in strong depression of respiration and ammonium excretion in calanoid copepods and euphausiids from the Eastern Tropical North Atlantic and the Eastern Tropical South Pacific. These physiological responses need to be taken into account when estimating DVM-mediated fluxes of carbon and nitrogen into OMZs.

scholarly journals Vertical distribution of planktic foraminifera through an oxygen minimum zone: how assemblages and test morphology reflect oxygen concentrations

2021 ◽  
Vol 18 (3) ◽  
pp. 977-992
Author(s):  
Catherine V. Davis ◽  
Karen Wishner ◽  
Willem Renema ◽  
Pincelli M. Hull
Keyword(s):  
Sediment Cores ◽  
Biogeochemical Cycles ◽  
Oxygen Minimum Zone ◽  
Global Ocean ◽  
Low Oxygen ◽  
Planktic Foraminifera ◽  
Morphometric Analyses ◽  
Minimum Zone ◽  
Global Biogeochemical Cycles ◽  
Oxygen Minimum

Abstract. Oxygen-depleted regions of the global ocean are rapidly expanding, with important implications for global biogeochemical cycles. However, our ability to make projections about the future of oxygen in the ocean is limited by a lack of empirical data with which to test and constrain the behavior of global climatic and oceanographic models. We use depth-stratified plankton tows to demonstrate that some species of planktic foraminifera are adapted to life in the heart of the pelagic oxygen minimum zone (OMZ). In particular, we identify two species, Globorotaloides hexagonus and Hastigerina parapelagica, living within the eastern tropical North Pacific OMZ. The tests of the former are preserved in marine sediments and could be used to trace the extent and intensity of low-oxygen pelagic habitats in the fossil record. Additional morphometric analyses of G. hexagonus show that tests found in the lowest oxygen environments are larger, more porous, less dense, and have more chambers in the final whorl. The association of this species with the OMZ and the apparent plasticity of its test in response to ambient oxygenation invites the use of G. hexagonus tests in sediment cores as potential proxies for both the presence and intensity of overlying OMZs.

scholarly journals Vertical distribution of planktic foraminifera through an Oxygen Minimum Zone: how assemblages and shell morphology reflect oxygen concentrations

2020 ◽  
Author(s):  
Catherine V. Davis ◽  
Karen Wishner ◽  
Willem Renema ◽  
Pincelli M. Hull
Keyword(s):  
Sediment Cores ◽  
Oxygen Minimum Zone ◽  
Shell Morphology ◽  
Global Ocean ◽  
Low Oxygen ◽  
Planktic Foraminifera ◽  
Morphometric Analyses ◽  
Minimum Zone ◽  
Global Biogeochemical Cycles ◽  
Oxygen Minimum

Abstract. Oxygen-depleted regions of the global ocean are rapidly expanding, with important implications for global biogeochemical cycles. However, our ability to make projections of a future deoxygenated ocean is limited by a lack of empirical data with which to test and constrain the behavior of global climatic and oceanographic models. We use depth-stratified plankton tows to demonstrate that some species of planktic foraminifera are adapted to life in the heart of the pelagic Oxygen Minimum Zone (OMZ). In particular, we identify two species, Globorotaloides hexagonus and Hastigerina parapelagica, living within the Eastern Tropical North Pacific OMZ. The shells of the former are preserved in marine sediments and could be used to trace the extent and intensity of low-oxygen pelagic habitats in the fossil record. Additional morphometric analyses of G. hexagonus show that shells found in the lowest oxygen environments are larger, more porous, less dense, and have more chambers in the final whorl. The association of this species with the OMZ and the apparent plasticity of its shell in response to ambient oxygenation invites the use of G. hexagonus shells in sediment cores as potential proxies for both the presence and intensity of overlying OMZs.

scholarly journals Indications for a ubiquitous dissolved pigment degradation product in subsurface waters of the global ocean

2011 ◽  
Vol 8 (5) ◽  
pp. 10697-10724
Author(s):  
R. Röttgers ◽  
B. P. Koch
Keyword(s):  
Degradation Product ◽  
Oxygen Minimum Zone ◽  
Particulate Fraction ◽  
Global Ocean ◽  
Red Fluorescence ◽  
Pigment Degradation ◽  
Fluorescence Measurements ◽  
Minimum Zone ◽  
Absorption Shoulder ◽  
Oxygen Minimum

Abstract. Measurements of light absorption by chromophoric dissolved organic matter (CDOM) from sub-surface waters of the tropical Atlantic and Pacific showed a distinct absorption shoulder at 410–415 nm, indicating an underlying absorption of a pigment. A similar absorption maximum at ~410 nm was also found in the particulate fraction and is usually attributed to absorption by respiratory pigments of heterotrophic unicellular organisms. The CDOM absorption shoulder was described earlier in the Indian Ocean at 600 m depth and was related to a "deep red fluorescence" found in the same depth, i.e. in the oxygen minimum zone (Breves et al., 2003; Broenkow et al., 1983). In our study, fluorescence measurements of pre-concentrated DOM samples confirmed that the absorption at ~410 nm was related to a specific fluorescence at 650 nm. The absorption characteristic of this specific fluorophor was examined by fluorescence emission/excitation analysis and this showed a clear excitation maximum at 415 nm (in methanol) that can explain the absorption shoulder in the CDOM spectra. The spectral characteristics of the substance found in the dissolved and particulate fraction did not match with those of chlorophyll a degradation products (as found in a sample from the sea surface) but can be explained by the occurrence of respiratory pigments from heterotrophs. Combining the observations of the "deep red fluorescence" and the 410 nm-absorption shoulder suggests that there are high concentrations of a pigment degradation product (cytochrome c) in DOM of all major oceans. Most pronouncedly we found this signal in the deep chlorophyll maximum and the oxygen minimum zone of tropical regions. The origin, chemical nature, turn-over rate, and fate of this molecule is so far unknown.

Temporally invariable bacterial community structure in the Arabian Sea oxygen minimum zone

2014 ◽  
Vol 73 (1) ◽  
pp. 51-67 ◽  
Author(s):  
A Jain ◽  
M Bandekar ◽  
J Gomes ◽  
D Shenoy ◽  
RM Meena ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Arabian Sea ◽  
Oxygen Minimum Zone ◽  
Minimum Zone ◽  
Oxygen Minimum
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