On the maverick Planctomycetes

FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(6), P. 739 - 760

Published: July 22, 2018

Planctomycetes are ubiquitous, environmentally and biotechnologically important bacteria that key players in global carbon nitrogen cycles. Ever since their first discovery the 1920s they seemed to blur prokaryote /eukaryote dichotomy. After initially being described as fungi reclassified later, were still thought feature a nucleus-like compartment surrounding highly condensed DNA. Also, an endocytosis-like uptake mechanism for macromolecules was described. Besides these eukaryotic hallmark traits, lack typical bacterial features such peptidoglycan cell wall or universal division protein FtsZ, while mostly dividing by polar budding instead of binary fission. Thus, speculated be ancestral both, eukaryotes. With advent novel microscopic techniques, along with development genetic tools Planctomycetes, some hypotheses revisited. Surprisingly, found possess comprise plan comparable other Gram-negative structure is rather invagination cytoplasmic membrane than cohesive compartment. These finding challenge idea ancestry phylum, now appear similar, yet distinct bacteria.

Language: Английский

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Host-microbe interactions in octocoral holobionts - recent advances and perspectives

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: April 2, 2018

Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from shallow tropics to Antarctic deep sea, providing habitat for numerous as well ecosystem services humans. In contrast holobionts reef-building scleractinian corals, octocorals have received relatively little attention, despite devastating effects disease outbreaks on many populations. Recent advances shown that possess remarkably stable bacterial communities geographical and temporal scales under environmental stress. This may be result their high capacity regulate microbiome through production antimicrobial quorum-sensing interfering compounds. Despite decades research relating octocoral-microbe interactions, a synthesis this expanding field has not been conducted date. We therefore provide an urgently needed review our current knowledge about octocoral holobionts. Specifically, we briefly introduce ecological role concept holobiont before detailed overviews (I) symbiosis between algal symbiont Symbiodinium; (II) main fungal, viral, taxa associated with octocorals; (III) dominance microbial assemblages by few species, stability these associations, evolutionary history host organism; (IV) diseases; (V) how use immune system fight pathogens; (VI) regulation its microbes; (VII) discovery natural products regulatory activities. Finally, present perspectives should move forward, recognition suitable model study coral-microbe symbioses.

Language: Английский

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High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: May 30, 2017

Coral reefs are a complex ecosystem consisting of coral animals and vast array associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses bacteria. Several studies have highlighted importance coral-associated bacteria their fundamental roles in fitness survival host animal. The scleractinian Porites lutea is one dominant reef-builders Indo-West Pacific. Currently, very little known about composition structure bacterial communities across P. reefs. purpose this study twofold: to demonstrate advantages using PacBio circular consensus sequencing technology microbial community investigate diversity lutea-associated microbiome Indo-Pacific. This first metagenomic marine environmental samples that utilises system capture full-length 16S rRNA sequences. We observed geographically distinct profiles between from Gulf Thailand Andaman Sea. Despite geographical impacts on coral-host interactions, we identified conserved were present consistently diverse reef habitats. Finally, demonstrated superior performance sequences resolving taxonomic uncertainty associates at species level.

Language: Английский

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Microalgae-bacteria interaction in palm oil mill effluent treatment

Journal of Water Process Engineering, Journal Year: 2020, Volume and Issue: 35, P. 101203 - 101203

Published: Feb. 28, 2020

Language: Английский

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Tuning up microbiome analysis to monitor WWTPs’ biological reactors functioning

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: March 5, 2020

Abstract Wastewater treatment plants (WWTPs) are necessary to protect ecosystems quality and human health. Their function relies on the degradation of organic matter nutrients from a water influent, prior effluent release into environment. In this work we studied bacterial community dynamics municipal WWTP with membrane bioreactor through 16S rRNA gene sequencing. The main phyla identified in wastewater were Proteobacteria , Bacteroidetes Chloroflexi Planctomycetes Actinobacteria . is located Spain and, like other temperate climate zones, temperature played major role assembly. Seasonal succession observed along two years sampling period, addition continual annual drift microbial populations. core was also studied, where small fraction sequence variants constituted large total abundance. This microbiome stability period likewise dissimilarity patterns gradient makes feature good candidate for new process control WWTPs.

Language: Английский

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Microbiomes of stony and soft deep-sea corals share rare core bacteria

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: June 10, 2019

Numerous studies have shown that bacteria form stable associations with host corals and focused on identifying conserved "core microbiomes" of bacterial associates inferred to be serving key roles in the coral holobiont. Because tend focus only stony (order Scleractinia) or soft Alcyonacea), it is currently unknown if there are shared by both. A meta-analysis was done 16S rRNA amplicon data from multiple generated via identical methodology allow direct comparisons across seven deep-sea corals, including both species: Anthothela grandiflora, sp., Lateothela Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, resedaeformis. Twenty-three operational taxonomic units (OTUs) were consistently present greater than 50% samples. Seven sequence variants (ASVs), five which corresponded a OTU, 30% samples species. majority sequences had close matches previously identified coral-associated bacteria. While known dominate tropical temperate microbiomes, Endozoicomonas extremely rare absent these corals. An OTU associated Lo. pertusa this study most similar those shallow-water while an spp. gorgonians. Bacterial been at level class Anthozoa (i.e., found shallow deep). These therefore hypothesized play important symbiotic highlighted for targeted future study. include taxa potential nitrogen sulfur cycling, detoxification, hydrocarbon degradation. There also some overlap kit contaminants need resolved. Rarely detected partitioned whether coral, finer clustering pattern reflects hosts' phylogeny.

Language: Английский

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Bacterial Communities in Tissues and Surficial Mucus of the Cold-Water Coral Paragorgia arborea

Frontiers in Marine Science, Journal Year: 2018, Volume and Issue: 5

Published: Oct. 18, 2018

Coral bacterial associates can play important functional roles for the holobiont, such as nitrogen cycling, nutrient processing, and supporting immunity. While bacteria found within microbiome of corals may benefit host, they also be linked to pathogenesis. In deep-sea, cold-water corals, like their warm shallow-water counterparts, host communities, but have received little attention due logistical constraints in sampling. particular, associated with surficial mucus not yet been investigated. Here, tissue samples Paragorgia arborea were collected from three submarine canyons along continental slope Gulf Maine. Bacterial DNA was extracted sequencing V6-V8 hypervariable region 16S rRNA gene performed using Illumina MiSeq. The communities P. compartments (tissue mucus) sampling locations (canyon) differed significantly composition. Proteobacteria, Tenericutes, Spirochaetes dominant phyla across majority coral samples, Gammaproteobacteria Alphaproteobacteria identified largest Proteobacteria contributors all samples. OTUs belonging taxa Spirochaeta, Mycoplasma, Flavobacteriaceae, Terasakiellaceae, Campylobacterales Rickettsiales biomarkers (bacterial more abundant a specific microhabitat) tissues, while Paracoccus biomarker mucus. Many recovered involved cycling. Representatives several families (Vibrionaceae, Campylobacteraceae, Rhodobacteraceae, Flavobacteraceae, Burkholderiaceae) previously reported diseased scleractinians, present rare taxa. Characterizing visibly healthy colonies provides benchmark groups holobiont. This is first characterization arborea, examining both tissue- mucus-specific communities.

Language: Английский

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Biogeographic Comparison of Lophelia-Associated Bacterial Communities in the Western Atlantic Reveals Conserved Core Microbiome

Frontiers in Microbiology, Journal Year: 2017, Volume and Issue: 8

Published: May 4, 2017

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa, a globally distributed scleractinian coral that creates critical three-dimensional habitat in deep ocean. The bacterial community associated with L. pertusa previously described by number of studies at sites Mediterranean Sea, Norwegian fjords, off Great Britain, and Gulf Mexico (GOM). However, use different methodologies prevents direct comparisons most cases. Our objectives were address intra-regional variation identify any conserved core community. We collected samples from three distinct colonies each four locations within western Atlantic: GOM one east coast United States. Amplicon libraries 16S rRNA genes generated using primers targeting V4-V5 hypervariable region 454 pyrosequencing. dominant phylum was Proteobacteria (75–96%). At family level, 80–95% sample comprised five groups: Pirellulaceae, Pseudonocardiaceae, Rhodobacteraceae, Sphingomonadaceae, unclassified Oceanospirillales. Principal coordinate analysis based weighted UniFrac distances showed clear distinction between Atlantic samples. Interestingly, replicate location did not always cluster together, indicating there is strong site-specific influence. community, 100% samples, dominated OTUs genera Novosphingobium Pseudonocardia, both known degraders aromatic hydrocarbons. sequence another member, Propionibacterium, also found prior Norway suggesting role as symbiont. By examining more than 40,000 sequences per sample, we identified sequences, whereas open had much higher proportion locally-consistent bacteria. Further, predictive functional profiling highlights potential for microbiome contribute chemoautotrophy, nutrient cycling, antibiotic production.

Language: Английский

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Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: March 17, 2017

Abstract Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that microbes may play a fundamental role in maintaining viable coral host via acquisition and recycling nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities three scleractinian from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula , Rhizotrochus typus . We found diverse, species-specific microbiomes, distinct surrounding seawater. Microbiomes were comprised few abundant bacteria, which constituted majority sequences (up 58% depending on species). In addition, high diversity rare bacteria (taxa at <1% abundance >90% all bacteria). Interestingly, identified anaerobic potentially providing metabolic functions low oxygen conditions, as well harboring potential degrade crude oil components. Considering presence gas fields these unlock this carbon source for host. conclusion, prevailing environmental conditions deep Sea (>20 °C, <2 mg L −1 ) require functional adaptations, our data suggest contribute functioning challenging environment.

Language: Английский

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Metabarcoding analysis of regional variation in gut contents of the copepod Calanus finmarchicus in the North Atlantic Ocean

Deep Sea Research Part II Topical Studies in Oceanography, Journal Year: 2020, Volume and Issue: 180, P. 104738 - 104738

Published: Jan. 20, 2020

Language: Английский

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