scholarly journals Molecular Detection of Fungal Communities in the Hawaiian Marine Sponges Suberites zeteki and Mycale armata

2008 ◽  
Vol 74 (19) ◽  
pp. 6091-6101 ◽  
Author(s):  
Zheng Gao ◽  
Binglin Li ◽  
Chengchao Zheng ◽  
Guangyi Wang
Keyword(s):  
Molecular Analysis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Terrestrial Ecosystems ◽  
Fungal Species ◽  
Marine Sponges ◽  
Fungal Communities ◽  
Sponge Species ◽  
Rrna Gene ◽  
Significant Group ◽  
Marine Habitats

ABSTRACT Symbiotic microbes play a variety of fundamental roles in the health and habitat ranges of their hosts. While prokaryotes in marine sponges have been broadly characterized, the diversity of sponge-inhabiting fungi has barely been explored using molecular approaches. Fungi are an important component of many marine and terrestrial ecosystems, and they may be an ecologically significant group in sponge-microbe interactions. This study tested the feasibility of using existing fungal primers for molecular analysis of sponge-associated fungal communities. None of the eight selected primer pairs yielded satisfactory results in fungal rRNA gene or internal transcribed spacer (ITS) clone library constructions. However, 3 of 10 denaturing gradient gel electrophoresis (DGGE) primer sets, which were designed to preferentially amplify fungal rRNA gene or ITS regions from terrestrial environmental samples, were successfully amplified from fungal targets in marine sponges. DGGE analysis indicated that fungal communities differ among different sponge species (Suberites zeteki and Mycale armata) and also vary between sponges and seawater. Sequence analysis of DGGE bands identified 23 and 21 fungal species from each of the two sponge species S. zeteki and M. armata, respectively. These species were representatives of 11 taxonomic orders and belonged to the phyla of Ascomycota (seven orders) and Basidiomycota (four orders). Five of these taxonomic orders (Malasseziales, Corticiales, Polyporales, Agaricales, and Dothideomycetes et Chaetothyriomcetes incertae sedis) have now been identified for the first time in marine sponges. Seven and six fungal species from S. zeteki and M. armata, respectively, are potentially new species because of their low sequence identity (≤98%) with their references in GenBank. Phylogenetic analysis indicated sponge-derived sequences were clustered into “marine fungus clades” with those from other marine habitats. This is the first report of molecular analysis of fungal communities in marine sponges, adding depth and dimension to our understanding of sponge-associated microbial communities.

scholarly journals Diversity of Bacteria in the Marine Sponge Aplysina fulva in Brazilian Coastal Waters

2009 ◽  
Vol 75 (10) ◽  
pp. 3331-3343 ◽  
Author(s):  
C. C. P. Hardoim ◽  
R. Costa ◽  
F. V. Ara�jo ◽  
E. Hajdu ◽  
R. Peixoto ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sampling Site ◽  
Marine Sponges ◽  
Sponge Species ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Gradient Gel Electrophoresis ◽  
Aplysina Fulva

ABSTRACT Microorganisms can account for up to 60% of the fresh weight of marine sponges. Marine sponges have been hypothesized to serve as accumulation spots of particular microbial communities, but it is unknown to what extent these communities are directed by the organism or the site or occur randomly. To address this question, we assessed the composition of specific bacterial communities associated with Aplysina fulva, one of the prevalent sponge species inhabiting Brazilian waters. Specimens of A. fulva and surrounding seawater were collected in triplicate in shallow water at two sites, Caboclo Island and Tartaruga beach, B�zios, Brazil. Total community DNA was extracted from the samples using “direct” and “indirect” approaches. 16S rRNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analyses of the total bacterial community and of specific bacterial groups—Pseudomonas and Actinobacteria—revealed that the structure of these assemblages in A. fulva differed drastically from that observed in seawater. The DNA extraction methodology and sampling site were determinative for the composition of actinobacterial communities in A. fulva. However, no such effects could be gleaned from total bacterial and Pseudomonas PCR-DGGE profiles. Bacterial 16S rRNA gene clone libraries constructed from directly and indirectly extracted DNA did not differ significantly with respect to diversity and composition. Altogether, the libraries encompassed 15 bacterial phyla and the candidate division TM7. Clone sequences affiliated with the Cyanobacteria, Chloroflexi, Gamma- and Alphaproteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were, in this order, most abundant. The bacterial communities associated with the A. fulva specimens were distinct and differed from those described in studies of sponge-associated microbiota performed with other sponge species.

scholarly journals Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4965 ◽  
Author(s):  
Mary T.H.D. Nguyen ◽  
Torsten Thomas
Keyword(s):  
Host Specificity ◽  
Horizontal Transmission ◽  
Critical Role ◽  
Fungal Species ◽  
Fungal Communities ◽  
Sponge Species ◽  
Fungal Community Composition ◽  
Potential Core ◽  
Community Profiling ◽  
Surrounding Seawater

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.

scholarly journals Only a Few Fungal Species Dominate Highly Diverse Mycofloras Associated with the Common Reed

2006 ◽  
Vol 72 (2) ◽  
pp. 1118-1128 ◽  
Author(s):  
Karin Neubert ◽  
Kurt Mendgen ◽  
Henner Brinkmann ◽  
Stefan G. R. Wirsel
Keyword(s):  
Niche Differentiation ◽  
Common Reed ◽  
Fungal Species ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Nonparametric Estimators ◽  
Single Host ◽  
Host Habitat ◽  
Nested Pcr Assays ◽  
Log Normal

ABSTRACT Plants are naturally colonized by many fungal species that produce effects ranging from beneficial to pathogenic. However, how many of these fungi are linked with a single host plant has not been determined. Furthermore, the composition of plant-associated fungal communities has not been rigorously determined. We investigated these essential issues by employing the perennial wetland reed Phragmites australis as a model. DNA extracted from roots, rhizomes, stems, and leaves was used for amplification and cloning of internal transcribed spacer rRNA gene fragments originating from reed-associated fungi. A total of 1,991 clones from 15 clone libraries were differentiated by restriction fragment length polymorphism analyses into 345 operational taxonomical units (OTUs). Nonparametric estimators for total richness (Chao1 and ACE) and also a parametric log normal model predicted a total of about 750 OTUs if the libraries were infinite. Sixty-two percent of the OTUs sequenced were novel at a threshold of 3%. Several of these OTUs represented undocumented fungal species, which also included higher taxonomic levels. In spite of the high diversity of the OTUs, the mycofloras of vegetative organs were dominated by just a few typical fungi, which suggested that competition and niche differentiation influence the composition of plant-associated fungal communities. This suggestion was independently supported by the results of nested PCR assays specifically monitoring two OTUs over 3 years, which revealed significant preferences for host habitat and host organ.

scholarly journals Characterization of a Culturable Alphaproteobacterial Symbiont Common to Many Marine Sponges and Evidence for Vertical Transmission via Sponge Larvae

2006 ◽  
Vol 72 (5) ◽  
pp. 3724-3732 ◽  
Author(s):  
Julie J. Enticknap ◽  
Michelle Kelly ◽  
Olivier Peraud ◽  
Russell T. Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Marine Sponges ◽  
Rrna Gene ◽  
Surrounding Water ◽  
Axinella Corrugata ◽  
Gradient Gel Electrophoresis ◽  
Related Group

ABSTRACT A closely related group of alphaproteobacteria were found to be present in seven genera of marine sponges from several locations and were shown to be transferred between sponge generations through the larvae in one of these sponges. Isolates of the alphaproteobacterium were cultured from the sponges Axinella corrugata, Mycale laxissima, Monanchora unguifera, and Niphates digitalis from Key Largo, Florida; Didiscus oxeata and Monanchora unguifera from Discovery Bay, Jamaica; an Acanthostronglyophora sp. from Manado, Indonesia; and Microciona prolifera from the Cheasapeake Bay in Maryland. Isolates were very similar to each other on the basis of 16S rRNA gene sequence (>99% identity) and are closely related to Pseudovibrio denitrificans. The bacterium was never isolated from surrounding water samples and was cultured from larvae of M. laxissima, indicating that it is a vertically transmitted symbiont in this sponge. Denaturing gradient gel electrophoresis, 16S rRNA gene clone library analysis, and fluorescent in situ hybridization with probes specific to the alphaproteobacterium confirmed the presence of this bacterium in the M. laxissima larvae. The alphaproteobacterium was densely associated with the larvae rather than being evenly distributed throughout the mesohyl. This is the first report of the successful culture of a bacterial symbiont of a sponge that is transferred through the gametes.

scholarly journals The Microbiology of Olive Mill Wastes

2013 ◽  
Vol 2013 ◽  
pp. 1-16 ◽  
Author(s):  
Spyridon Ntougias ◽  
Kostas Bourtzis ◽  
George Tsiamis
Keyword(s):  
Microbial Communities ◽  
High Strength ◽  
Terrestrial Ecosystems ◽  
Fungal Species ◽  
Rrna Gene ◽  
Human Pathogens ◽  
Olive Mill Waste ◽  
Olive Mill Wastes ◽  
Mill Waste ◽  
Olive Mill

Olive mill wastes (OMWs) are high-strength organic effluents, which upon disposal can degrade soil and water quality, negatively affecting aquatic and terrestrial ecosystems. The main purpose of this review paper is to provide an up-to-date knowledge concerning the microbial communities identified over the past 20 years in olive mill wastes using both culture-dependent and independent approaches. A database survey of 16S rRNA gene sequences (585 records in total) obtained from olive mill waste environments revealed the dominance of members ofAlphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes,andActinobacteria. Independent studies confirmed that OMW microbial communities’ structure is cultivar dependant. On the other hand, the detection of fecal bacteria and other potential human pathogens in OMWs is of major concern and deserves further examination. Despite the fact that the degradation and detoxification of the olive mill wastes have been mostly investigated through the application of known bacterial and fungal species originated from other environmental sources, the biotechnological potential of indigenous microbiota should be further exploited in respect to olive mill waste bioremediation and inactivation of plant and human pathogens. The implementation of omic and metagenomic approaches will further elucidate disposal issues of olive mill wastes.

Characterization of bacterial and fungal communities in composted biosolids over a 2 year period using denaturing gradient gel electrophoresis

2009 ◽  
Vol 55 (4) ◽  
pp. 375-387 ◽  
Author(s):  
Amy Novinscak ◽  
Nadine J. DeCoste ◽  
Céline Surette ◽  
Martin Filion
Keyword(s):  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Fungal Species ◽  
Fungal Communities ◽  
Whole Process ◽  
Agricultural Applications ◽  
Gradient Gel Electrophoresis ◽  
Microbial Groups ◽  
Key Microorganisms

Composting is a microbial process that converts organic waste into a nutrient-rich end product used in horticultural and agricultural applications. The diversity and long-term succession of microorganisms found in composted biosolids has been less characterized than other composts. In this study, bacterial and fungal communities found in composted biosolids aging from 1 to 24 months were studied using denaturing gradient gel electrophoresis (DGGE) and sequencing. The results revealed high levels of diversity, where 53 bacterial species belonging to 10 phyla and 21 fungal species belonging to 4 phyla were identified. Significant differences were observed when comparing the bacterial DGGE patterns of young compost samples, whereas no differences were observed in samples over 8 months. For fungal patterns, no significant differences were observed during the first 4 months of composting, but the diversity then significantly shifted until 24 months. The results indicate that patterns of bacterial species vary during the first few months of composting, whereas fungal patterns generally vary throughout the whole process, except during early stages. The description of the main microbial groups found in composted biosolids could find various applications, including the discovery of biotechnologically relevant microorganisms and the development of novel markers allowing quantitative monitoring of key microorganisms.

scholarly journals BIODIVERSITY ASSESSMENT OF MICROORGANISMS ASSOCIATED WITH TWO MARINE SPONGES (Haliclona oculata AND Amphius huxleyi) COLLECTED AT THE LANG CO BAY OF VIETNAM

2018 ◽  
Vol 18 (3) ◽  
pp. 286-295
Author(s):  
Ton That Huu Dat ◽  
Pham Viet Cuong ◽  
Tran Thi Dung Dung ◽  
Vu Thi Thu Huyen ◽  
Nguyen Thi Kim Cuc
Keyword(s):  
Illumina Miseq ◽  
Taxonomic Diversity ◽  
Marine Sponges ◽  
Sponge Species ◽  
Rrna Gene ◽  
Sponge Tissue ◽  
Biodiversity Assessment ◽  
Haliclona Oculata ◽  
Reference Sequences ◽  
The 16S Rrna Gene

Sponges (Phylum Porifera) are ancient sedentary and filter-feeding animals which harbour very diverse and abundant associated microbial community in their tissues with density up to 40–50% of sponge tissue volume. In this study, the diversity of associated microorganisms with two marine sponges Haliclona oculata and Amphius huxleyi collected at the Lang Co bay of Vietnam was assessed by analysis of hypervariable V3 and V4 regions of the 16S rRNA gene using Illumina MiSeq system. The taxonomic diversity of sponge-associated microorganisms was classified to different taxonomic levels (kingdom, phylum, class, order, family, and genus). Based on Bayesian classification method and reference sequences derived from Greengenes database, the associated microorganisms in studied sponges were assigned to 17 phyla (H. oculata) and 13 phyla (A. huxleyi). Many microbial taxa were detected in two sponge species, however, they were distinctive by the abundance. Proteobacteria was the most dominant phylum in both sponge species, and all of 4 classes Epsilonproteobacteria, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were found in H. oculata and A. huxleyi.

scholarly journals Real-Time Quantitative PCR for Assessment of Abundance of Pseudoalteromonas Species in Marine Samples

2004 ◽  
Vol 70 (4) ◽  
pp. 2373-2382 ◽  
Author(s):  
Torben L. Skovhus ◽  
Niels B. Ramsing ◽  
Carola Holmström ◽  
Staffan Kjelleberg ◽  
Ingela Dahllöf
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Green Alga ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Marine Animals ◽  
Real Time Quantitative Pcr ◽  
Marine Samples ◽  
Marine Habitats ◽  
Pcr Method

ABSTRACT A real-time quantitative PCR (RTQ-PCR) method for measuring the abundance of Pseudoalteromonas species in marine samples is presented. PCR primers targeting a Pseudoalteromonas-specific region of the 16S rRNA gene were tested at three different levels using database searches (in silico), a selection of pure cultures (in vitro), and a combined denaturing gradient gel electrophoresis and cloning approach on environmental DNA (in situ). The RTQ-PCR method allowed for the detection of SYBR Green fluorescence from double-stranded DNA over a linear range spanning six orders of magnitude. The detection limit was determined as 1.4 fg of target DNA (1,000 gene copies) measured in the presence of 20 ng of nontarget DNA from salmon testes. In this study, we discuss the importance of robust post-PCR analyses to overcome pitfalls in RTQ-PCR when samples from different complex marine habitats are analyzed and compared on a nonroutine basis. Representatives of the genus Pseudoalteromonas were detected in samples from all investigated habitats, suggesting a widespread distribution of this genus across many marine habitats (e.g., seawater, rocks, macroalgae, and marine animals). Three sample types were analyzed by RTQ-PCR to determine the relative abundance of Pseudoalteromonas ribosomal DNA (rDNA) compared to the total abundance of eubacterial rDNA. The rDNA fractions of Pseudoalteromonas compared to all Eubacteria were 1.55% on the green alga Ulva lactuca, 0.10% on the tunicate Ciona intestinalis, and 0.06% on the green alga Ulvaria fusca.

scholarly journals Investigation of Oscillatoria spongeliae-Dominated Bacterial Communities in Four Dictyoceratid Sponges

2005 ◽  
Vol 71 (11) ◽  
pp. 7366-7375 ◽  
Author(s):  
Christian P. Ridley ◽  
D. John Faulkner ◽  
Margo G. Haygood
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Marine Invertebrates ◽  
Marine Sponges ◽  
Sponge Species ◽  
Epithelial Tissue ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Oscillatoria Spongeliae

ABSTRACT Certain species of marine sponges in the order Dictyoceratida harbor large populations of the cyanobacterial symbiont Oscillatoria spongeliae in the mesohyl (interior) of the sponge. We show that in four of these sponge species (Lamellodysidea herbacea, Lamellodysidea chlorea, Lendenfeldia chondrodes, and Phyllospongia papyracea) from Palau there is a consistent community of α-proteobacteria in addition to O. spongeliae that fall within the Rhodobacter group based on 16S rRNA gene analysis. Some of the α-proteobacteria in Lendenfeldia chondrodes and P. papyracea but not in the Lamellodysidea spp. contained site-specific insertions in the 16S rRNA gene. Reverse transcription-PCR experiments demonstrated that the largest insertion found in this study (63 bp) is present in the mature rRNA. Lendenfeldia chondrodes was the only sponge found to have another cyanobacterium in the tissue, a Synechocystis sp. We found that the Synechocystis sp. was present in both the pinacoderm (surface epithelial tissue) and mesohyl, in contrast to O. spongeliae, which was only found in the mesohyl through the use of specific fluorescence in situ hybridization experiments. Of the four sponge species, only P. papyracea was found to contain a significant number of γ-proteobacteria. These results demonstrate that O. spongeliae-dominated bacterial communities in different sponge species can vary considerably and increase our understanding of the bacterial communities found in marine invertebrates.

scholarly journals Fungal Communities Respond to Long-Term CO2Elevation by Community Reassembly

2015 ◽  
Vol 81 (7) ◽  
pp. 2445-2454 ◽  
Author(s):  
Qichao Tu ◽  
Mengting Yuan ◽  
Zhili He ◽  
Ye Deng ◽  
Kai Xue ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Fungal Community ◽  
Geodesic Distance ◽  
Fungal Species ◽  
Fungal Communities ◽  
Rrna Gene ◽  
28S Rrna ◽  
Ecological Network ◽  
Community Reassembly

ABSTRACTFungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO2(eCO2), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO2, and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO2for 12 years. Long-term eCO2did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; ∼27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO2were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO2increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO2network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO2, especially with increased plant biomass and NH4+availability. This study provided novel insights into how eCO2shapes soil fungal communities in grassland ecosystems.

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