Bacterial community structure and diversity along the halocline of Tyro deep-sea hypersaline anoxic basin

Purpose: Tyro is a deep hypersaline anoxic basin (DHAB) located at the seafloor of the Eastern Mediterranean sea. Tyro hosts a stratified eukaryotic microbiome moving from seawater to the brine, but no reports are available on its prokaryotic community. We provide the first snapshot of the bacterial community structure in Tyro brine, seawaterbrine interface, and the overlaying deep seawater. Methods: In this study, we combined the use of molecular analyses, i.e., DNA fingerprinting and 16S rRNA pyrosequencing for the description of the bacterial community structure and taxonomy. PiCRUST2 was used to infer information on the prokaryotes functional diversity. A culture-dependent approach was applied to enrich bacteria of interest for marine biotechnology. Results: Bacterial communities sharply clustered moving from the seawater to the Tyro brine, in agreement with the abrupt increase of salinity values. Moreover, specific taxonomic groups inhabited the seawater-brine interface compared to the overlaying seawater and their identification revealed converging taxonomy with other DHABs in the Eastern Mediterranean sea. Functional traits inferred from the prokaryote taxonomy in the upper interface and the overlaying seawater indicated metabolic pathways for the synthesis of osmoprotectants, likely involved in bacterial adaptation to the steep increasing salinity. Metabolic traits related to methane and methylated compounds and to hydrocarbon degradation were also revealed in the upper interface of Tyro. The overall capability of the Tyro microbiome for hydrocarbon metabolism was confirmed by the isolation of hydrocarbonoclastic bacteria in the sediments. Conclusions: Our results suggest that Tyro seawater-brine interface hosts a specific microbiome adapted to the polyextreme condition typical of DHABs with potential metabolic features that could be further explored for the characterization of the metabolic network connecting the brine with the deep seawater through the chemocline. Moreover, Tyro could be a reservoir of culturable microbes endowed with functionalities of interest for biotechnological applications like hydrocarbon bioremediation

Delayed larval development in Anopheles mosquitoes deprived of Asaia bacterial symbionts

<p>Abstract</p> <p>Background</p> <p>In recent years, acetic acid bacteria have been shown to be frequently associated with insects, but knowledge on their biological role in the arthropod host is limited. The discovery that acetic acid bacteria of the genus <it>Asaia</it> are a main component of the microbiota of <it>Anopheles stephensi</it> makes this mosquito a useful model for studies on this novel group of symbionts. Here we present experimental results that provide a first evidence for a beneficial role of <it>Asaia</it> in <it>An. stephensi</it>.</p> <p>Results</p> <p>Larvae of <it>An. stephensi</it> at different stages were treated with rifampicin, an antibiotic effective on wild-type <it>Asaia</it> spp., and the effects on the larval development were evaluated. Larvae treated with the antibiotic showed a delay in the development and an asynchrony in the appearance of later instars. In larvae treated with rifampicin, but supplemented with a rifampicin-resistant mutant strain of <it>Asaia</it>, larval development was comparable to that of control larvae not exposed to the antibiotic. Analysis of the bacterial diversity of the three mosquito populations confirmed that the level of <it>Asaia</it> was strongly decreased in the antibiotic-treated larvae, since the symbiont was not detectable by PCR-DGGE (denaturing gradient gel electrophoresis), while <it>Asaia</it> was consistently found in insects supplemented with rifampicin plus the antibiotic-resistant mutant in the diet, and in those not exposed to the antibiotic.</p> <p>Conclusions</p> <p>The results here reported indicate that <it>Asaia</it> symbionts play a beneficial role in the normal development of <it>An. stephensi</it> larvae.</p

Developmental stages and gut microenvironments influence gut microbiota dynamics in the invasive beetle Popillia japonica Newman (Coleoptera: Scarabaeidae)

Popillia japonica Newman (Coleoptera: Scarabaeidae) is a highly polyphagous invasive beetle originating from Japan. This insect is highly resilient and able to rapidly adapt to new vegetation. Insect?associated microorganisms can play important roles in insect physiology, helping their hosts to adapt to changing conditions and potentially contributing to an insect's invasive potential. Such symbiotic bacteria can be part of a core microbiota that is stably transmitted throughout the host's life cycle or selectively recruited from the environment at each developmental stage. The aim of this study was to investigate the origin, stability and turnover of the bacterial communities associated with an invasive population of P. japonica from Italy. Our results demonstrate that soil microbes represent an important source of gut bacteria for P. japonica larvae, but as the insect develops, its gut microbiota richness and diversity decreased substantially, paralleled by changes in community composition. Notably, only 16.75% of the soil bacteria present in larvae are maintained until the adult stage. We further identified the micro?environments of different gut sections as an important factor shaping microbiota composition in this species, likely due to differences in pH, oxygen availability and redox potential. In addition, P. japonica also harboured a stable bacterial community across all developmental stages, consisting of taxa well known for the degradation of plant material, namely the families Ruminococcacae, Christensenellaceae and Lachnospiraceae. Interestingly, the family Christensenallaceae had so far been observed exclusively in humans. However, the Christensenellaceae operational taxonomic units found in P. japonica belong to different taxonomic clades within this family

A 2000-Year-Old <i>Bacillus stercoris</i> Strain Sheds Light on the Evolution of Cyclic Antimicrobial Lipopeptide Synthesis

Some bacteria (notably the genera Bacillus and Clostridium) have the capacity to form endospores that can survive for millions of years in isolated habitats. The genomes of such ancient bacteria provide unique opportunities to understand bacterial evolution and metabolic capabilities over longer time scales. Herein, we sequenced the genome of a 2000-year-old bacterial strain (Mal05) isolated from intact apple seeds recovered during archaeological excavations of a Roman villa in Italy. Phylogenomic analyses revealed that this strain belongs to the species Bacillus stercoris and that it is placed in an early-branching position compared to most other strains of this species. Similar to other Bacillus species, B. stercoris Mal05 had been previously shown to possess antifungal activity. Its genome encodes all the genes necessary for the biosynthesis of fengycin and surfactin, two cyclic lipopeptides known to play a role in the competition of Bacilli with other microorganisms due to their antimicrobial activity. Comparative genomics and analyses of selective pressure demonstrate that these genes are present in all sequenced B. stercoris strains, despite the fact that they are not under strong purifying selection. Hence, these genes may not be essential for the fitness of these bacteria, but they can still provide a competitive advantage against other microorganisms present in the same environment

Complete Genome Sequence of Rhynchophorus ferrugineus Endocytobiont "Candidatus Nardonella dryophthoridicola" Strain NardRF

We report the complete genome sequence and annotation of "Candidatus Nardonella dryophthoridicola" strain NardRF, obtained by sequencing its host bacteriome, Rhynchophorus ferrugineus, using Oxford Nanopore technology.We report the complete genome sequence and annotation of “Candidatus Nardonella dryophthoridicola” strain NardRF, obtained by sequencing its host bacteriome, Rhynchophorus ferrugineus, using Oxford Nanopore technology

Microbial Community of the Acidogenic Fermentation of Urban Waste: Effect of the Hydrodynamic Cavitation Pre-treatment

International audiencePurpose This study aims at understanding how the acidogenic fermentation microbial community was impacted by the hydrodynamic cavitation (HC) pre-treatment of the substrates' mixture, constituted by waste-activated sludge and vegetable waste 1:1 on a TVS basis.Methods HC was performed with power = 8 kW, P = 1.4-1.5 bar, Q(mixture) of 25-30 L/min, 1550-1650 rpm, duration: 30 min. Fermentation tests were conducted on cavitated (CAV) and not cavitated (NCAV) mixture at T = 37 degrees C inside 4 L reactors in batch mode, then switched to semi-continuous with an OLR of 8 kg(TVS) m(-3) d(-1). Microbial community was characterized by 16S rRNA sequencing at the beginning and end of the pseudo-steady-state. Ecological diversity and clustering among the samples were determined by beta diversity, Venn diagram, and non-metric multi-dimensional scaling (NMDS) analysis.Results Cavitation was efficient in substrates' hydrolyzation but resulted in a lower microbial diversity of 3.85 (Shannon Index) and VFAs concentration of 12.9 gCOD(VFA) L-1 in the anaerobically fermented cavitated mixture (AF-CAV), respect to 4.54 and 18.2 gCOD(VFA) L-1 in the anaerobically fermented not cavitated mixture (AF-NCAV), respectively. NMDS analysis showed that AF-CAV and AF-NCAV samples formed two different clusters, with VFAs concentration as the only significant factor explaining their difference (R-2 = 1, Pr > r = 0.04167). Functional redundancy among community members probably allowed to maintain a stable VFAs composition despite the microbial community variation observed at the end of the test.Conclusion The insights here provided on the effects of HC confirm the fundamental role played by microbial community in acidogenic fermentation processes and underline its importance in evaluating the effect of substrates' pre-treatment

The bacterial community associated to an italian population of psacothea hilaris: A preliminary study

The yellow-spotted longicorn beetle, Psacothea hilaris (Pascoe) (Coleoptera Cerambycidae), native to eastern Asia, is an invasive species for Europe, where it is present since 2005 as a pest of Morus and Ficus spp. Up to date, no study on the bacterial community associated with P. hilaris has been carried out. The aim of the present work is to characterize the bacterial community associated to an Italian population of P. hilaris collected on F. carica L. through a culture-independent method (i.e., 454 pyrosequenc-ing) targeting the 16S rRNA gene. The DNA used for bacterial characterization has been extracted from the whole abdomen of 15 adults (seven males and eight females) sampled on the host plant immediately after their emergence in Alserio (Como, Italy) between August and September 2012. The sequencing strategy led to a total of ≈ 2,350 bacterial 16S rRNA gene sequences that have been clustered into 141 bacterial operational taxonomic units. Results shown that the bacterial community was dominated by Proteobacteria (86%) belonging to Oxalobacteraceae and Enterobacteriaceae (respectively 36.4% and 34.8%). Pantoea resulted the most abundant genus (28.4%), and the other relevant bacterial genera associated with P. hilaris are Ralstonia (18.6%), Methy-lobacterium (3%), Lactococcus (2%) and Propionibacterium (1.4%)

Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella

Diversity and composition of lepidopteran microbiotas are poorly investigated, especially across the different developmental stages. To improve this knowledge, we characterize the microbiota among different developmental stages of the Indian meal moth, Plodia interpunctella, which is considered one of the major pest of commodities worldwide. Using culture-independent approach based on Illumina 16S rRNA gene sequencing we characterized the microbiota of four developmental stages: eggs, first-, and last-instar larvae, and adult. A total of 1022 bacterial OTUs were obtained, showing a quite diversified microbiota associated to all the analyzed stages. The microbiotas associated with P. interpunctella resulted almost constant throughout the developmental stages, with approximately 77% of bacterial OTUs belonging to the phylum of Proteobacteria. The dominant bacterial genus is represented by Burkholderia (∼64%), followed by Propionibacterium, Delftia, Pseudomonas, and Stenotrophomonas. A core bacterial community, composed of 139 OTUs, was detected in all the developmental stages, among which 112 OTUs were assigned to the genus Burkholderia. A phylogenetic reconstruction, based on the 16S rRNA, revealed that our Burkholderia OTUs clustered with Burkholderia cepacia complex, in the same group of those isolated from the hemipterans Gossyparia spuria and Acanthococcus aceris. The functional profiling, predicted on the base of the bacterial 16S rRNA, indicates differences in the metabolic pathways related to metabolism of amino acids between preimaginal and adult stages. We can hypothesize that bacteria may support the insect host during preimaginal stages

Draft genome sequence of the hydrocarbon-degrading bacterium Alcanivorax dieselolei KS-293 isolated from surface seawater in the Eastern Mediterranean Sea

We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5

Acetic acid bacteria as symbionts of insects

Acetic acid bacteria (AAB) are being increasingly described as associating with different insect species that rely on sugar-based diets. AAB have been found in several insect orders, among them Diptera, Hemiptera, and Hymenoptera, including several vectors of plant, animal, and human diseases. AAB have been shown to associate with the epithelia of different organs of the host, they are able to move within the insect’s body and to be transmitted horizontally and vertically. Here, we review the ecology of AAB and examine their relationships with different insect models including mosquitoes, leafhoppers, and honey bees. We also discuss the potential use of AAB in symbiont-based control strategies, such as “Trojan-horse” agents, to block the transmission of vector-borne diseases