Author
Paraskevi N. Polymenakou
Bio: Paraskevi N. Polymenakou is an academic researcher from University of Crete. The author has contributed to research in topics: Mediterranean sea & Total organic carbon. The author has an hindex of 22, co-authored 50 publications receiving 2533 citations.
Papers published on a yearly basis
Papers
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TL;DR: It is shown that in contrast to what was expected from the sharp decrease in organic carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both the eastern and the western basins of the Mediterranean Sea is similarly high.
Abstract: Deep-sea ecosystems represent the largest biome of the global biosphere, but knowledge of their biodiversity is still scant. The Mediterranean basin has been proposed as a hot spot of terrestrial and coastal marine biodiversity but has been supposed to be impoverished of deep-sea species richness. We summarized all available information on benthic biodiversity (Prokaryotes, Foraminifera, Meiofauna, Macrofauna, and Megafauna) in different deepsea ecosystems of the Mediterranean Sea (200 to more than 4,000 m depth), including open slopes, deep basins, canyons, cold seeps, seamounts, deep-water corals and deep-hypersaline anoxic basins and analyzed overall longitudinal and bathymetric patterns. We show that in contrast to what was expected from the sharp decrease in organic carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both the eastern and the western basins of the Mediterranean Sea is similarly high. All of the biodiversity components, except Bacteria and Archaea, displayed a decreasing pattern with increasing water depth, but to a different extent for each component. Unlike patterns observed for faunal abundance, highest negative values of the slopes of the biodiversity patterns were observed for Meiofauna, followed by Macrofauna and Megafauna. Comparison of the biodiversity associated with open slopes, deep basins, canyons, and deep-water corals showed that the deep basins were the least diverse. Rarefaction curves allowed us to estimate the expected number of species for each benthic component in different bathymetric ranges. A large fraction of exclusive species was associated with each specific habitat or ecosystem. Thus, each deep-sea ecosystem contributes significantly to overall biodiversity. From theoretical extrapolations we estimate that the overall deep-sea Mediterranean biodiversity (excluding prokaryotes) reaches approximately 2805 species of which about 66% is still undiscovered. Among the biotic components investigated (Prokaryotes excluded), most of the unknown species are within the phylum Nematoda, followed by Foraminifera, but an important fraction of macrofaunal and megafaunal species also remains unknown. Data reported here provide new insights into the patterns of biodiversity in the deep-sea Mediterranean and new clues for future investigations aimed at identifying the factors controlling and threatening deep-sea biodiversity.
335 citations
TL;DR: An overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies is provided and future trends in the field are provided with respect to tools and technologies currently under development.
Abstract: Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of “metagenomics”, often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.
323 citations
TL;DR: The presence of aerosolized bacteria in small size particles may have significant implications to human health via intercontinental transportation of pathogens.
Abstract: In the last decade, the increase of desertification has resulted in a concomitant intensification of atmospheric dust loadings (Moulin and Chiapello 2006). Furthermore, El Nino events have coincided with increased flux of Saharan dust across the Atlantic (Prospero and Lamb 2003). Moulin et al. (1997) have estimated that dust flux from the Saharan-Sahel region to the atmosphere is approximately 1 billion tons/year. In addition to the effect of airborne dust on visibility and Earth’s climate through the processes of atmospheric radiation balance, photochemistry, and cloud formation, these dusts can also exert a direct impact on human health (Taylor 2002). The World Health Organization (WHO) has identified drought and dust storm activity in the sub-Saharan region of Africa as causing regional outbreaks of meningococcal meningitis (in 1996 there were ~ 250,000 cases and 25,000 deaths) (Griffin 2007; WHO 2003).
Recently, dust events have been shown to introduce a significant pulse of microorganisms (Griffin 2007) and other microbiological materials (i.e., cellular fragments, fungal spores) into the atmosphere (Jaenicke 2005). However, to a large extent, the distribution of microorganisms in different particle sizes has been ignored, although it could have significant implications regarding the dispersion of microorganisms around the world. Study of the particle size distribution of microorganisms will enhance our knowledge a) of the species of microbes able to be transported over long distances and thus affect remote areas, and b) how climate change could increase the health risk from microbial pathogens.
Traditionally, the detection and enumeration of airborne microorganisms has been conducted using light microscopy and/or culture-based methods. However, these analyses are time-consuming and laborious, lack sensitivity and specificity (Stetzenbach et al. 2004), and offer just a glimpse of the biological agents present (< 1% of environmental bacteria can be cultivated) (Amann et al. 1995; Hugenholtz et al. 1998; Pace 1997). The development of various techniques based on community molecular analysis has freed researchers from culturing biases and allowed characterization of community structure [e.g., 16S and 18S ribosomal RNA (rRNA) genes for bacteria and microeukaryotes, respectively] (Amann et al. 1995).
In the present study, we used molecular-based methods to analyze the microbial components of bioaerosol samples collected from the atmosphere of a coastal city (Heraklion, Crete) of the eastern Mediterranean Sea during an intense African dust event. The study area is subject to frequent and severe Saharan dust events (Gerasopoulos et al. 2006). Air sampling was carried out during 24–25 February 2006 when large quantities of dust were exported from northern Africa to southern Europe (NASA 2006). The aim of the study was to investigate the microbial quality of size-distributed aerosol particles during a dust storm by using a high-volume pump equipped with a five-stage cascade impactor for efficient genomic DNA extraction (Radosevich et al. 2002). The composition of the airborne microorganisms was determined by cloning and sequencing the 16S rRNA genes. To the best of our knowledge, this is the first report of size-distributed airborne bacteria during a Saharan storm using molecular-based methods.
245 citations
TL;DR: A 2.5-m-thick chemocline with a steep NaCl gradient at 3.3 km within the water column betweeen Bannock anoxic hypersaline brine and overlying sea water is reported, supporting some of the most biomass-rich and active microbial communities in the deep sea.
Abstract: The chemical composition of the Bannock basin has been studied in some detail. We recently showed that unusual microbial populations, including a new division of Archaea (MSBL1), inhabit the NaCl-rich hypersaline brine. High salinities tend to reduce biodiversity, but when brines come into contact with fresher water the natural haloclines formed frequently contain gradients of other chemicals, including permutations of electron donors and acceptors, that may enhance microbial diversity, activity and biogeochemical cycling. Here we report a 2.5-m-thick chemocline with a steep NaCl gradient at 3.3 km within the water column betweeen Bannock anoxic hypersaline brine and overlying sea water. The chemocline supports some of the most biomass-rich and active microbial communities in the deep sea, dominated by Bacteria rather than Archaea, and including four major new divisions of Bacteria. Significantly higher metabolic activities were measured in the chemocline than in the overlying sea water and underlying brine; functional analyses indicate that a range of biological processes is likely to occur in the chemocline. Many prokaryotic taxa, including the phylogenetically new groups, were confined to defined salinities, and collectively formed a diverse, sharply stratified, deep-sea ecosystem with sufficient biomass to potentially contribute to organic geological deposits.
200 citations
University of New South Wales1, University of California, San Diego2, University of Auckland3, UPRRP College of Natural Sciences4, Wageningen University and Research Centre5, Shanghai Jiao Tong University6, National University of Ireland, Galway7, Victoria University of Wellington8, University of Notre Dame9, Paul Sabatier University10, University of Alabama11, Institut national de la recherche agronomique12, University of Haifa13, Australian Institute of Marine Science14, Tel Aviv University15, University of North Carolina at Wilmington16, University of Oldenburg17, University of British Columbia18, Stony Brook University19, University of Lisbon20, University of Maryland Center for Environmental Science21, King Abdullah University of Science and Technology22, Leibniz Institute of Marine Sciences23, University of Queensland24
TL;DR: This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge- associated rare biosphere.
Abstract: Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
179 citations
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University of Southern Mississippi1, University of California, San Diego2, Atlantic Oceanographic and Meteorological Laboratory3, University of California, San Francisco4, Indiana University5, IBM6, Massachusetts Institute of Technology7, Broad Institute8, Harvard University9, Northern Arizona University10, Pacific Northwest National Laboratory11, Argonne National Laboratory12, University of Illinois at Chicago13, University of Colorado Boulder14, Cooperative Institute for Research in Environmental Sciences15, University of Southern California16, University of Chicago17, Michigan State University18
TL;DR: A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
Abstract: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
1,676 citations
14 May 2010
TL;DR: Overall spatial and temporal patterns of species diversity and major changes and threats were assessed, and temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity.
Abstract: Trabajo presentado en el 39th CIESM Congress, celebrado en Venecia, Italia, del 10 al 14 de mayo de 2010
1,379 citations
TL;DR: This review summarizes what is known and unknown about AOM on earth and its key catalysts, the anaerobic methanotrophic archaea clades and their bacterial partners.
Abstract: Methane is the most abundant hydrocarbon in the atmosphere, and it is an important greenhouse gas, which has so far contributed an estimated 20% of postindustrial global warming. A great deal of biogeochemical research has focused on the causes and effects of the variation in global fluxes of methane throughout earth's history, but the underlying microbial processes and their key agents remain poorly understood. This is a disturbing knowledge gap because 85% of the annual global methane production and about 60% of its consumption are based on microbial processes. Only three key functional groups of microorganisms of limited diversity regulate the fluxes of methane on earth, namely the aerobic methanotrophic bacteria, the methanogenic archaea, and their close relatives, the anaerobic methanotrophic archaea (ANME). The ANME represent special lines of descent within the Euryarchaeota and appear to gain energy exclusively from the anaerobic oxidation of methane (AOM), with sulfate as the final electron accept...
1,373 citations
Spanish National Research Council1, Dalhousie University2, University of British Columbia3, University of Freiburg4, University of Montpellier5, University of Genoa6, Aristotle University of Thessaloniki7, National Institute of Oceanography, India8, Oranim Academic College9, WorldFish10, University of Seville11, University of the Basque Country12, University of Thessaly13
TL;DR: In this article, the authors combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists.
Abstract: The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well.
This abstract has been translated to other languages (File S1).
1,326 citations
TL;DR: A review of the current knowledge on major categories of primary biological aerosol particles (PBAP): bacteria and archaea, fungal spores and fragments, pollen, viruses, algae and cyanobacteria, biological crusts and lichens and others like plant or animal fragments and detritus is presented in this article.
Abstract: Atmospheric aerosol particles of biological origin are a very diverse group of biological materials and structures, including microorganisms, dispersal units, fragments and excretions of biological organisms. In recent years, the impact of biological aerosol particles on atmospheric processes has been studied with increasing intensity, and a wealth of new information and insights has been gained. This review outlines the current knowledge on major categories of primary biological aerosol particles (PBAP): bacteria and archaea, fungal spores and fragments, pollen, viruses, algae and cyanobacteria, biological crusts and lichens and others like plant or animal fragments and detritus. We give an overview of sampling methods and physical, chemical and biological techniques for PBAP analysis (cultivation, microscopy, DNA/RNA analysis, chemical tracers, optical and mass spectrometry, etc.). Moreover, we address and summarise the current understanding and open questions concerning the influence of PBAP on the atmosphere and climate, i.e. their optical properties and their ability to act as ice nuclei (IN) or cloud condensation nuclei (CCN). We suggest that the following research activities should be pursued in future studies of atmospheric biological aerosol particles: (1) develop efficient and reliable analytical techniques for the identification and quantification of PBAP; (2) apply advanced and standardised techniques to determine the abundance and diversity of PBAP and their seasonal variation at regional and global scales (atmospheric biogeography); (3) determine the emission rates, optical properties, IN and CCN activity of PBAP in field measurements and laboratory experiments; (4) use field and laboratory data to constrain numerical models of atmospheric transport, transformation and climate effects of PBAP. Keywords: primary biological atmospheric aerosol; climate; cloud condensation nuclei; biology; atmospheric ice nuclei (Published: 22 February 2012) Citation: Tellus B 2012, 64 , 15598, DOI: 10.3402/tellusb.v64i0.15598
1,034 citations