Whale-fall Research Articles

Abundance and functional diversity of riboswitches in microbial communities.

BackgroundSeveral recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not biased towards cultured organisms. It is a good source for estimation of the abundance of genes and regulatory structures in both known and unknown members of microbial communities. In this study we consider the distribution of RNA regulatory structures, riboswitches, in the Sargasso Sea, Minnesota Soil and Whale Falls metagenomes.ResultsOver three hundred riboswitches were found in about 2 Gbp metagenome DNA sequences. The abundabce of riboswitches in metagenomes was highest for the TPP, B12 and GCVT riboswitches; the S-box, RFN, YKKC/YXKD, YYBP/YKOY regulatory elements showed lower but significant abundance, while the LYS, G-box, GLMS and YKOK riboswitches were rare. Regions downstream of identified riboswitches were scanned for open reading frames. Comparative analysis of identified ORFs revealed new riboswitch-regulated functions for several classes of riboswitches. In particular, we have observed phosphoserine aminotransferase serC (COG1932) and malate synthase glcB (COG2225) to be regulated by the glycine (GCVT) riboswitch; fatty acid desaturase ole1 (COG1398), by the cobalamin (B12) riboswitch; 5-methylthioribose-1-phosphate isomerase ykrS (COG0182), by the SAM-riboswitch. We also identified conserved riboswitches upstream of genes of unknown function: thiamine (TPP), cobalamine (B12), and glycine (GCVT, upstream of genes from COG4198).ConclusionThis study demonstrates applicability of bioinformatics to the analysis of RNA regulatory structures in metagenomes.

A biodiversity-based approach to development of performance enzymes: Applied metagenomics and directed evolution

Industrial BiotechnologyVol. 1, No. 4 MethodsA biodiversity-based approach to development of performance enzymes: Applied metagenomics and directed evolutionEric J. Mathur, Gerardo Toledo, Brian D. Green, Mircea Podar, Toby H. Richardson, Michael Kulwiec, and Hwai W. ChangEric J. MathurSearch for more papers by this author, Gerardo ToledoSearch for more papers by this author, Brian D. GreenSearch for more papers by this author, Mircea PodarSearch for more papers by this author, Toby H. RichardsonSearch for more papers by this author, Michael KulwiecSearch for more papers by this author, and Hwai W. ChangSearch for more papers by this authorPublished Online:23 Dec 2005https://doi.org/10.1089/ind.2005.1.283AboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetailsCited byEngineering biosynthetic enzymes for industrial natural product synthesis1 January 2020 | Natural Product Reports, Vol. 37, No. 8Evidence of selective pressure in whale fall microbiome proteins and its potential application to industryMarine Genomics, Vol. 45Deep-sea hydrothermal vent ecosystem principles: Identification of ecosystem processes, services and communication of valueMarine Policy, Vol. 101Identification of lipolytic enzymes isolated from bacteria indigenous to Eucalyptus wood species for application in the pulping industryBiotechnology Reports, Vol. 15Accessing Carboxylesterase Diversity from Termite Hindgut Symbionts through Metagenomics4 October 2012 | Journal of Molecular Microbiology and Biotechnology, Vol. 22, No. 5Culturability and Secondary Metabolite Diversity of Extreme Microbes: Expanding Contribution of Deep Sea and Deep-Sea Vent Microbes to Natural Product Discovery1 May 2010 | Marine Biotechnology, Vol. 13, No. 1Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism15 March 2010 | Marine Drugs, Vol. 8, No. 3Library Construction For Protein Engineering8 March 2010 Volume 1Issue 4Dec 2005 InformationCopyright 2005, Mary Ann Liebert, Inc.To cite this article:Eric J. Mathur, Gerardo Toledo, Brian D. Green, Mircea Podar, Toby H. Richardson, Michael Kulwiec, and Hwai W. Chang.A biodiversity-based approach to development of performance enzymes: Applied metagenomics and directed evolution.Industrial Biotechnology.Dec 2005.283-287.http://doi.org/10.1089/ind.2005.1.283Published in Volume: 1 Issue 4: December 23, 2005PDF download

Unusual benthic fauna associated with a whale fall in Monterey Canyon, California

On February 6, 2002, we discovered an unusual assemblage of deep-sea animals associated with a well-preserved carcass of a gray whale (Eschrichtius robustus) at 2891m depth in the axis of Monterey Canyon, California. The 9–10m long carcass was found approximately 31km off shore, where it settled to the bottom against the northern wall of the canyon's sedimented floor. This carcass delivered approximately 20,000kg of organic material to a typically food-limited seafloor. Particularly noteworthy were the low occurrence of large mobile scavengers, the large number of opportunistic deep-sea species, and an abundance of unusual polychaetes. Two of these polychaetes, a spionid and a siboglinid, are new to science. Since this discovery, we visited the whale fall on two subsequent occasions (March and October 2002) to document faunal community changes in one of the deepest large food falls known to date.

The impact of whale falls on nematode abundance in the deep sea

Abundance of nematode assemblages from the sediment surrounding an experimentally implanted whale carcass in the Santa Cruz Basin were investigated at 1.5 and 18 months after placement. Samples were taken at 0, 1, 3, 9 and 30 m distance away from the carcass. Abundance is positively correlated with distance from the carcass out to at least 30 m. Analyses of nematode abundance at 18 months after implantation showed a non-linear inverse pattern to that of the macrofauna implying that enhanced macrofaunal activity immediately around the carcass was decreasing nematode abundance through predation or competition. The increased nematode abundance at 30 m after 18 months may be a response to organic enrichment from the whale fall occurring where macrofaunal abundance no longer limits nematode densities.

Use of 210Pb/ 226Ra disequilibria in the dating of deep-sea whale falls

Deep-sea whale falls, in particular the skeletal remains of whales that have sunk to the seafloor, are remarkable temporary reducing habitats. Reduced chemical species created by anaerobic microbial decay of lipid and organic compounds within the whale bone matrix fuel chemosynthetic-based communities, including bacteria, mussels, limpets, snails, and clams. Many of these species exhibit taxonomic affinities to other chemosynthetic deep-sea organisms colonizing hydrothermal vents and cold seeps. Knowledge of the timescales of whale fall community succession and persistence of these assemblages is needed to reliably estimate the abundance of whale fall habitats and to understand the dynamics of the whale fall communities and their potential roles as stepping stones for sulfophilic species. We have developed a radiochemical method based on 210Pb/ 226Ra disequilibria for estimating the ages of seafloor whale bone communities. Measurements of 210Pb/ 226Ra performed on known age bone samples yielded radioisotope ages in good agreement with the known ages. Our results indicate that this technique is valid for bones 10–85 years old (time since cetacean death). This technique, applied to multiple bones of unknown age whale falls taken from Monterey Canyon, Santa Catalina Basin, and San Nicholas Basin, constrained the upper limit ages of these systems (in 2002) to 6.3±1.0 years, 44.0±7.0 to 53.4±8.3 years, and 66.4±9.6 to 82.6±11 years, respectively. These ages were in reasonable agreement with faunal and/or skeletal observations. In addition, a preliminary lipid degradation rate was calculated for the Santa Catalina Basin whale fall using an independent time series and calibrated to the radiochemically determined age. Both radiochemical and lipid degradation evidence suggest that the whale fall microhabitat is able to support life for many decades.

High species richness in deep-sea chemoautotrophic whale skeleton communities

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 260:109-114 (2003) - doi:10.3354/meps260109 High species richness in deep-sea chemoautotrophic whale skeleton communities Amy R. Baco1,2,*, Craig R. Smith1 1Department of Oceanography, 1000 Pope Road, Honolulu, Hawaii 96822, USA 2Present address: Woods Hole Oceanographic Institution, Biology Department, MS#33 2-14 Redfield, Woods Hole, Massachusetts 02543, USA *Email: abaco@whoi.edu ABSTRACT: While biodiversity in deep-sea soft sediments appears to be high, little is known about diversity levels on deep-sea hard substrates. To determine the contribution of potentially abundant whale-skeleton habitats to deep-sea biodiversity, we compare the local macrofaunal species richness and composition on 3 sulfide-rich whale skeletons to assemblages from vents, seeps, and other deep-sea hard substrates. Based on rarefaction curves, whale skeleton diversity is higher than diversity in any other deep-sea hard substrate habitat. The average local species richness (185 spp.) on single chemoautotrophic whale skeletons approaches known levels of global cold-seep macrofaunal species richness (229 spp.), and exceeds the richness of the most speciose vent field known (121 spp.). Species richness on the whale skeletons is also substantially higher than on other deep-sea non-reducing hard substrates, such as manganese nodules and rocks. Richness levels approach those in deep-sea soft sediments and exceed some shallow-water hard substrates. This high species richness may be explained by unusually high trophic diversity on whale bones due to the presence of sulphophiles, generalized organic-enrichment respondents, whale-bone consumers, and background hard-substrate fauna such as suspension and deposit feeders. High species richness levels on whale skeletons and deep-sea sponge stalks suggest deep-sea hard substrates may harbor higher levels of diversity than previously recognized. KEY WORDS: Whale fall · Species richness · Biodiversity · Deep sea · Hard substrate Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 260. Online publication date: September 30, 2003 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2003 Inter-Research.

Vestimentiferan on a whale fall.

Discovery of chemosynthetic communities associated with whale bones led to the hypothesis that whale falls may serve as stepping-stones for faunal dispersal between disjunct hydrothermal vents and cold seeps on the ocean floor (1). The initial observation was followed by a faunal inventory that revealed a diverse assemblage of microbes and invertebrates, supported by chemoautotrophic production, living in close proximity to whale remains (2, 3). To date, the conspicuous absence from whale falls of vestimentiferan tubeworms (a predominant constituent of eastern Pacific vent and seep habitats) has been a major objection to the stepping-stone hypothesis (4-5). We report the first evidence of a vestimentiferan tubeworm associated with a whale fall (Fig. 1). The tubeworm, Escarpia spicata, was identified by morphological criteria and DNA sequence data from a portion of the mitochondrial cytochrome oxidase C subunit I (COI) gene. Additionally, the bacterial endosymbiont in the tubeworm possessed a 16S rRNA gene that was similar to that of endosymbionts from vestimentiferans in sedimented cold-seep environments.

Evidence for the microbial basis of a chemoautotrophic invertebrate community at a whale fall on the deep seafloor: bone-colonizing bacteria and invertebrate endosymbionts.

To explore the microbial basis for a remarkable macrofaunal community at the site of a whale skeleton on the seafloor of the Santa Catalina Basin, we obtained samples of whale bone, bone-colonizing invertebrates, microbial mats, and the dominant fauna in the adjacent sulfide-rich sediments during Alvin expeditions in 1988 and 1991. Invertebrate tissues were examined by transmission electron microscopy (TEM) and mats and bone-penetrating bacteria by epifluorescence microscopy (EM). Tissues from the dominant bivalve Vesicomya c.f. gigas, the mytilid mussel Idasola washingtonia, and selected gastropods and limpets were also assayed chemically for enzymes diagnostic of sulfur- and methane-based chemoautotrophy and for stable carbon isotopic composition. Results of all analyses were consistent with dominant sulfur-based endosymbioses in the clam and mussel (the first record of endosymbiosis in the genus Idasola) and the general absence of methane symbioses at the site, strengthening the analogy of the whale-skeleton faunal community to those known from distant Pacific hydrothermal vent sites. Examples of minor endosymbionts, either nitrifying or methanotrophic cells according to internal membrane structures by TEM, raised the possibility of a supplemental mode of nutrition to the clam, or means to remove ammonia in the gill tissue, in the event of significant changes in the chemical environment.