Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species.

Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown.

Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges.

Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species.

Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies.

Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has increased during the last years, the vast majority of marine diversity are rather unexplored. Moreover, most studies focused on the entire microbial community and thus do not assess the active fraction of the microbial community.

Seasonal and Zonal Succession of Bacterial Communities in North Sea Salt Marsh Sediments.

Benthic microbial communities of intertidal zones perform important biogeochemical processes and provide accessible nutrients for higher organisms. To unravel the ecosystem services of salt marsh microbial communities, we analyzed bacterial diversity and metabolic potential along the land-sea transition zone on seasonal scales on the German North Sea Island of Spiekeroog. Analysis of bacterial community was based on amplicon sequencing of 16S rRNA genes and -transcripts.

Probiotic supplementation for neonates with congenital gastrointestinal surgical conditions: guidelines for future research.

Our pilot RCT found that probiotic supplementation with the three-strain bifidobacterial product (B. breve M-16V, B. longum subsp.

Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts.

The diversity and function of sponge-associated symbionts is now increasingly understood; however, we lack an understanding of how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here, we performed a metatransciptomic analysis on three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidizing Ca.

Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome.

Microbial communities are major drivers of global elemental cycles in the oceans due to their high abundance and enormous taxonomic and functional diversity. Recent studies assessed microbial taxonomic and functional biogeography in global oceans but microbial functional biogeography remains poorly studied. Here we show that in the near-surface Atlantic and Southern Ocean between 62°S and 47°N microbial communities exhibit distinct taxonomic and functional adaptations to regional environmental conditions.

Probiotic supplementation in neonates with congenital gastrointestinal surgical conditions: a pilot randomised controlled trial.

Objective: To evaluate whether probiotic supplementation attenuates gut-dysbiosis in neonates with congenital gastrointestinal surgical conditions (CGISC).

Methods: Sixty-one neonates (≥35 weeks gestation) with CGISC were randomised to receive daily supplementation with a triple-strain bifidobacterial probiotic (n = 30) or placebo (n = 31) until discharge. Stool microbiota was analysed using 16S ribosomal RNA gene sequencing on samples collected before (T1), 1 week (T2), and 2 weeks (T3) after supplementation and before discharge (T4).

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences.

Background: Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic composition. However, the accuracy of these tools relies on functional information derived from genomes available in public databases, which are often not representative of the microorganisms present in the studied ecosystem.

Taxonomic, functional and expression analysis of viral communities associated with marine sponges.

Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of 'virus-laden' seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome.

Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae.

Horizontal gene transfer (HGT) is thought to be an important driving force for microbial evolution and niche adaptation and has been show in vitro to occur frequently in biofilm communities. However, the extent to which HGT takes place and what functions are being transferred in more complex and natural biofilm systems remains largely unknown. To address this issue, we investigated here HGT and enrichment of gene functions in the biofilm community of the common kelp (macroalgae) Ecklonia radiata in comparison to microbial communities in the surrounding seawater.

Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts.

The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth phylogenetic analyses, metatranscriptomics, and fluorescence in situ hybridisation microscopy.

Impact of Viral Lysis on the Composition of Bacterial Communities and Dissolved Organic Matter in Deep-Sea Sediments.

Viral lysis is a main mortality factor for bacteria in deep-sea sediments, leading to changing microbial community structures and the release of cellular components to the environment. Nature and fate of these compounds and the role of viruses for microbial diversity is largely unknown. We investigated the effect of viruses on the composition of bacterial communities and the pool of dissolved organic matter (DOM) by setting up virus-induction experiments using mitomycin C with sediments from the seafloor of the Bering Sea.

Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast.

Humpback whales endure several months of fasting while undertaking one of the longest annual migrations of any mammal, which depletes the whales' energy stores and likely compromises their physiological state. Airway microbiota are linked to respiratory health in mammals. To illuminate the dynamics of airway microbiota in a physiologically challenged mammal, we investigated the bacterial communities in the blow of East Australian humpback whales at two stages of their migration: at the beginning (n = 20) and several months into their migration (n = 20), using barcoded tag sequencing of the bacterial 16S rRNA gene.

The intestinal virome in children with cystic fibrosis differs from healthy controls.

Intestinal bacterial dysbiosis is evident in children with cystic fibrosis (CF) and intestinal viruses may be contributory, given their influence on bacterial species diversity and biochemical cycles. We performed a prospective, case-control study on children with CF and age and gender matched healthy controls (HC), to investigate the composition and function of intestinal viral communities. Stool samples were enriched for viral DNA and RNA by viral extraction, random amplification and purification before sequencing (Illumina MiSeq).

Metagenome Assembly and Metagenome-Assembled Genome Sequences from a Historical Oil Field Located in Wietze, Germany.

Crude oil-polluted sites are a global threat, raising the demand for remediation worldwide. Here, we investigated a crude oil metagenome from a former borehole in Wietze, Germany, and reconstructed 42 metagenome-assembled genomes, many of which contained genes involved in crude oil degradation with a high potential for bioremediation purposes.

Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves.

Cacao ( L.) is one of the most economically important crops worldwide. Despite the important role of endophytes for plant growth and health, very little is known about the effect of agroforestry management systems on the endophyte communities of .

Gut microbiota in neonates with congenital gastrointestinal surgical conditions: a prospective study.

Background: There is limited information on gut microbiota of neonates with congenital gastrointestinal surgical conditions (CGISCs) available.

Methods: This study compared stool microbiota and short-chain fatty acids (SCFAs) of 37 term infants with CGISCs with 36 term healthy infants (HIs). Two stool samples were collected from each infant: as soon as possible after birth (week 1) and 10-14 days of life (week 2).

Gut Microbiota in Children With Cystic Fibrosis: A Taxonomic and Functional Dysbiosis.

Intestinal dysbiosis has been observed in children with cystic fibrosis (CF), yet the functional consequences are poorly understood. We investigated the functional capacity of intestinal microbiota and inflammation in children with CF. Stool samples were collected from 27 children with CF and 27 age and gender matched healthy controls (HC) (aged 0.

Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands.

Green islands (the re-greening of senescent leaf tissues) are particularly evident on leaves infected with fungal pathogens. To date, there is only a limited number of studies investigating foliar endophytic microorganisms in phytopathogen-infected leaves. Here, we analysed bacterial and fungal endophyte communities in leaves without green islands (control leaves; CL), within green island areas (GLA) and the surrounding yellow leaf areas (YLA) of leaves with green islands of Acer campestre and A.

Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated .

are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges , cf. , and Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus and one novel genus, for which we propose the names " Nitrosopumilus hexadellus," " Nitrosopumilus detritiferus," and " Cenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured).

Distinct relationships between fluorescence in situ hybridization and 16S rRNA gene- and amplicon-based sequencing data of bacterioplankton lineages.

Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and amplicon sequencing of the total (16S rRNA gene) and potentially active (16S rRNA transcripts), community are the major state of the art approaches for assessing the composition of bacterial communities in marine pelagic and other ecosystems. However, CARD-FISH and amplicon sequencing methods have not yet been directly compared to assess the composition of bacterioplankton communities. Therefore, these approaches were used to study the composition of bacterial communities in two North Sea seawater mesocosm experiments supplemented with diatom-derived organic matter (OM).

Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean.

Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean.

The Majority of Active in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions.

General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range.