scholarly journals Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico)

2016 ◽  
Author(s):  
Estelle Couradeau ◽  
Daniel Roush ◽  
Brandon Scott Guida ◽  
Ferran Garcia-Pichel
Keyword(s):  
Puerto Rico ◽  
Microbial Communities ◽  
Intertidal Zone ◽  
Substrate Preference ◽  
Marine Habitats ◽  
Genetic Sampling ◽  
Phylogenetic Level ◽  
Isla De Mona ◽  
Close Relatives ◽  
High Diversity

Abstract. Endolithic microbial communities are prominent features of intertidal marine habitats, where they colonize a variety of substrates, contributing to their erosion. Almost two centuries worth of naturalistic studies focused on a few true-boring (euendolithic) phototrophs, but substrate preference has received little attention. The Isla de Mona (Puerto Rico) intertidal zone offers a unique setting to investigate substrate specificity of endolithic communities since various phosphate rock, limestone, and dolostone outcrops occur there. High-throughput 16S rDNA genetic sampling, enhanced by targeted cultivation, revealed that, while euendolithic cyanobacteria were dominant, the communities were invariably of high diversity, well beyond that reported in traditional studies, and implying an unexpected metabolic complexity, potentially contributed by secondary colonizers. While the overall community composition did not show differences traceable to the nature of the mineral substrate, we detected specialization among particular euendolithic cyanobacterial clades towards the type of substrate they excavate, but only at the OTU phylogenetic level, implying that close relatives have specialized recurrently into particular substrates. The cationic mineral component was determinant in this preference, calling for the existence in nature of alternatives to the boring mechanism described in culture that is based exclusively on transcellular calcium transport.

scholarly journals Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico)

2017 ◽  
Vol 14 (2) ◽  
pp. 311-324 ◽  
Author(s):  
Estelle Couradeau ◽  
Daniel Roush ◽  
Brandon Scott Guida ◽  
Ferran Garcia-Pichel
Keyword(s):  
Puerto Rico ◽  
Microbial Communities ◽  
Substrate Preference ◽  
Operational Taxonomic Units ◽  
Marine Habitats ◽  
Genetic Sampling ◽  
Phylogenetic Level ◽  
Isla De Mona ◽  
Close Relatives ◽  
High Diversity

Abstract. Endolithic microbial communities are prominent features of intertidal marine habitats, where they colonize a variety of substrates, contributing to their erosion. Almost 2 centuries worth of naturalistic studies focused on a few true-boring (euendolithic) phototrophs, but substrate preference has received little attention. The Isla de Mona (Puerto Rico) intertidal zone offers a unique setting to investigate substrate specificity of endolithic communities since various phosphate rock, limestone and dolostone outcrops occur there. High-throughput 16S rDNA genetic sampling, enhanced by targeted cultivation, revealed that, while euendolithic cyanobacteria were dominant operational taxonomic units (OTUs), the communities were invariably of high diversity, well beyond that reported in traditional studies and implying an unexpected metabolic complexity potentially contributed by secondary colonizers. While the overall community composition did not show differences traceable to the nature of the mineral substrate, we detected specialization among particular euendolithic cyanobacterial clades towards the type of substrate they excavate but only at the OTU phylogenetic level, implying that close relatives have specialized recurrently into particular substrates. The cationic mineral component was determinant in this preference, suggesting the existence in nature of alternatives to the boring mechanism described in culture that is based exclusively on transcellular calcium transport.

scholarly journals Removal of Pharmaceuticals and Personal Care Products during Water Recycling: Microbial Community Structure and Effects of Substrate Concentration

2014 ◽  
Vol 80 (8) ◽  
pp. 2440-2450 ◽  
Author(s):  
Kathryn M. Onesios-Barry ◽  
David Berry ◽  
Jody B. Proescher ◽  
I. K. Ashok Sivakumar ◽  
Edward J. Bouwer
Keyword(s):  
Water Treatment ◽  
Microbial Communities ◽  
Personal Care Products ◽  
Treatment Plant ◽  
Soil Aquifer Treatment ◽  
Personal Care ◽  
Wetting And Drying ◽  
Biological Removal ◽  
Close Relatives ◽  
Wetting And Drying Cycle

ABSTRACTMany pharmaceuticals and personal care products (PPCPs) have been shown to be biotransformed in water treatment systems. However, little research exists on the effect of initial PPCP concentration on PPCP biotransformation or on the microbial communities treating impacted water. In this study, biological PPCP removal at various concentrations was assessed using laboratory columns inoculated with wastewater treatment plant effluent. Pyrosequencing was used to examine microbial communities in the columns and in soil from a soil aquifer treatment (SAT; a method of water treatment prior to reuse) site. Laboratory columns were supplied with different concentrations (0.25, 10, 100, or 1,000 μg liter−1) of each of 15 PPCPs. Five PPCPs (4-isopropyl-3-methylphenol [biosol],p-chloro-m-xylenol, gemfibrozil, ketoprofen, and phenytoin) were not removed at any tested concentrations. Two PPCPs (naproxen and triclosan) exhibited removals independent of PPCP concentration. PPCP removal efficiencies were dependent on initial concentrations for biphenylol,p-chloro-m-cresol, chlorophene, diclofenac, 5-fluorouracil, ibuprofen, and valproic acid, showing that PPCP concentration can affect biotransformation. Biofilms from sand samples collected from the 0.25- and 10-μg liter−1PPCP columns were pyrosequenced along with SAT soil samples collected on three consecutive days of a wetting and drying cycle to enable comparison of these two communities exposed to PPCPs. SAT communities were similar to column communities in taxonomy and phylotype composition, and both were found to contain close relatives of known PPCP degraders. The efficiency of biological removal of PPCPs was found to be dependent on the concentration at which the contamination occurs for some, but not all, PPCPs.

scholarly journals Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography–Mass Spectrometry

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Emilia M. Sogin ◽  
Erik Puskás ◽  
Nicole Dubilier ◽  
Manuel Liebeke
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Coral Reef ◽  
Microbial Communities ◽  
Chemical Interaction ◽  
Heterotrophic Bacterium ◽  
Gas Chromatography Mass Spectrometry ◽  
Mangrove Sediment ◽  
Marine Microorganisms ◽  
Marine Habitats

ABSTRACT Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats limits the nontargeted analyses of the ocean exometabolome using mass spectrometry (MS). Current methods require salt removal prior to sample measurements, which can alter the molecular composition of the metabolome and limit the types of compounds detected by MS. To overcome these limitations, we developed a gas chromatography MS (GC-MS) method that avoids sample altering during salt removal and that detects metabolites down to nanomolar concentrations from less than 1 ml of seawater. We applied our method (SeaMet) to explore marine metabolomes in vitro and in vivo. First, we measured the production and consumption of metabolites during the culture of a heterotrophic bacterium, Marinobacter adhaerens. Our approach revealed successional uptake of amino acids, while sugars were not consumed. These results show that exocellular metabolomics provides insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered high concentrations of sugars and fatty acids, compounds predicted to play a key role for the abundant and diverse microbial communities in coral reef and mangrove sediments. Our data demonstrate that SeaMet advances marine metabolomics by enabling a nontargeted and quantitative analysis of marine metabolites, thus providing new insights into nutrient cycles in the oceans. IMPORTANCE Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other “omics” (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats.

scholarly journals Hydrogen production bySulfurospirillumspp. enables syntrophic interactions of Epsilonproteobacteria

2017 ◽  
Author(s):  
Stefan Kruse ◽  
Tobias Goris ◽  
Martin Westermann ◽  
Lorenz Adrian ◽  
Gabriele Diekert
Keyword(s):  
Hydrogen Production ◽  
Microbial Communities ◽  
Electron Donor ◽  
Alternative Energy ◽  
E Coli ◽  
Group 4 ◽  
Marine Habitats ◽  
Anoxic Environments ◽  
Pyruvate:Ferredoxin Oxidoreductase ◽  
Hydrogen Oxidizing Bacteria

AbstractHydrogen-producing bacteria are of environmental and biotechnological importance in anoxic environments, since hydrogen is an important electron donor for prokaryotes and of interest as an alternative energy source. Epsilonproteobacteria, inhabiting ecologically, clinically or biotechnologically relevant environments, are currently considered to be hydrogen-oxidizing bacteria exclusively. Here, we report hydrogen production for a genus of free-living Epsilonproteobacteria,Sulfurospirillumspp. inhabiting sediments, wastewater plants, bioelectrodes, oil reservoirs, contaminated areas, or marine habitats. The amount of hydrogen production was largely different in two subgroups ofSulfurospirillumspp., represented byS. cavoleiandS. multivorans. The former is shown to be the more potent hydrogen producer and excretes acetate as sole organic acid, while the latter exhibited a more flexible fermentation, producing additionally lactate and succinate. The observed hydrogen production could be assigned to a group 4 hydrogenase similar to Hydrogenase 4 (Hyf) inE. coli. We propose thatSulfurospirillumspp. produce molecular hydrogen with electrons derived from pyruvate oxidation by pyruvate:ferredoxin oxidoreductase and reduced ferredoxin. This hypothesis is supported by comparative proteome data, in which both PFOR and ferredoxin as well as hydrogenase 4 are up-regulated. A co-culture experiment withS. multivoransandMethanococcus voltaecultivated with lactate as sole substrate shows a syntrophic interaction between both organisms, since the former cannot grow fermentatively on lactate alone and the latter relies on hydrogen as electron donor. This opens up new perspectives on microbial communities, since Epsilonproteobacteria could play a yet unrecognized role as hydrogen producers in anoxic microbial communities.

scholarly journals The Marine Benthic Algal Flora of Puerto Rico, I. Ochrophyta: Phaeophyceae, Pelagophyceae, and Xanthophyceae

2021 ◽  
Author(s):  
David L. Ballantine ◽  
James N. Norris ◽  
Hector Ruiz
Keyword(s):  
Puerto Rico ◽  
Algal Flora ◽  
Benthic Species ◽  
Marine Communities ◽  
Marine Habitats ◽  
Species Type ◽  
Reproductive Anatomy ◽  
One New Species ◽  
Locality Information

This treatment is a taxonomic study of the benthic species of Ochrophyta known from Puerto Rico, Caribbean Sea. In all, 3 classes, 10 orders, 16 families, 33 genera, and 77 species occur in the benthic marine communities in Puerto Rico. Of these, three species of <i>Sargassum </i>are found only as unattached and free-floating. A brief summary of phycological studies in Puerto Rico and ecological descriptions of the most common marine habitats are presented. Along with date, place, and author(s) of valid publication for all genera and species, type locality information and descriptive accounts of vegetative morphological and reproductive anatomy are provided. Distribution of each species is given, and where relevant, comments on their habitat and their taxonomic and nomenclatural status are discussed. A key to the genera and keys to species within genera are included. Either an in situ or other illustration accompanies most species. Two new geographical distribution records for Puerto Rico and a description of one new species, <i>Lobophora brooksii</i> D. L. Ballant. et J. N. Norris, are included. <br>

scholarly journals Gastropod Density and Diversity in the Intertidal Zone of Malalayang Beach, Manado

2020 ◽  
Vol 10 (3) ◽  
pp. 121
Author(s):  
Sheyrel Tongkeles ◽  
Fransine B. Manginsela ◽  
Jety K. Rangan ◽  
Alex D. Kambey
Keyword(s):  
Intertidal Zone ◽  
Diversity Index ◽  
Line Transect ◽  
Random Numbers ◽  
Total Density ◽  
Gastropod Species ◽  
Transect Line ◽  
Line Transects ◽  
High Diversity

This study held in Malalayang Beach Manado, aims to determine  the density and diversity of Gastropods on the Malalayang coast of Manado. So the research objective is to find out the density and diversity of  Gastropods in Malalayang Beach, Manado. The study using the line transect technique with 50 cm x 50 cm sized. The transect line is placed perpendicular to the coastline. The distance between the line transects is 20 meters. On each transect line 5 squares are placed. The distance between squares is determined using random numbers. Gastropod species found in Malalayang Beach Manado consist of  31 species and 17 genus, each consisting of the Archaeogastropoda that consists of 3 species, Mesogastropoda consists of  9 species, and the Order of the Neogastropoda of 19 species. The total density of Gastropods in Malalayang Beach in Manado is 6.27 individuals / m2 with diversity of 3.07, according to the criteria for diversity index of Malalayang coast having high diversity. Based on this, it is suggested that Manado Malalayang Beach can be maintained and carried out management that considers the feasibility of the environment as one of the requirements for sustainable development.Keywords: Gastropods, Density, Species DiversityABSTRAK Penelitian ini dilakukan di Pantai Malalayang Manado,berkaitan dengan permasalahan yang dikemukakan bagaimanakah kepadatan dan keanekaragaman Gastropoda di pantai Malalayang Manado. Maka tujuan penelitian adalah Mengetahui kepadatan dan keanekaragaman Gastropoda di Pantai Malalayang Manado. Pengumpulan data dengan pendekatan Teknik line transect menggunakan kuadrat berukuran 50cm x 50cm. Line transect diletakkan tegak lurus dengan garis pantai. Jarak antara line transect sebesar 20 meter. Pada masing- masing line transect diletakkan 5 kuadrat. Jarak antar kuadrat ditentukan dengan menggunakan angka acak. Spesies Gastropoda yang ditemukan di Pantai Malalayang Manado terdiri dari 31 spesies dan 17 genera yang masing-masing terdiri dari Ordo Archaeogastropoda 3 spesies, Ordo Mesogastropoda 9 spesies, dan Ordo Neogastropoda 19 spesies. Kepadatan total Gastropoda di Pantai Malalayang Manado 6.27 individu/m2 dengan keanekaragaman 3,07, Menurut kriteria indeks keanekaragaman pantai Malalayang memiliki keanekaragaman yang tinggi. Berdasarkan hal tersebut, maka disarankan agar Pantai Malalayang Manado dapat dijaga dan dilakukan pengelolaan yang mempertimbangkan sskelayakan lingkungan sebagai salah satu syarat pembangunan berkelanjutan.Kata kunci: Gastropoda, Kepadatan, Keanekaragaman Jenis

A new species and a new record of Sphaeroma Bosc, 1802 (Sphaeromatidae: Isopoda: Crustacea) from intertidal marine habitats of the Persian Gulf

Zootaxa ◽  
2010 ◽  
Vol 2631 (1) ◽  
pp. 1 ◽  
Author(s):  
VALIALLAH KHALAJI-PIRBALOUTY ◽  
JOHANN-WOLFGANG WÄGELE
Keyword(s):  
New Species ◽  
Indian Ocean ◽  
Persian Gulf ◽  
Intertidal Zone ◽  
New Record ◽  
Marine Habitats ◽  
Strait Of Hormuz ◽  
The Persian Gulf ◽  
A New Species

Two species of Sphaeroma (Sphaeromatidae: Isopoda) from the Iranian coasts of the Persian Gulf were studied and described. Sphaeroma khalijfarsi sp. nov. is described from the intertidal zone of the Strait of Hormuz. This species is distinguished by the smooth pereonites; pleon without prominent tubercles and bearing some scattered small tubercles; pleotelson with numerous scattered small tubercles and well upturned posterior margins. Sphaeroma walkeri Stebbing, 1905 is reported from Kish and Qeshm Islands and from the southern coasts of Iran. Among the non-Indian Ocean species, Sphaeroma intermedium Baker, 1926 is transferred to genus Lekanesphera Verhoeff, 1943.

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