Tenebrio molitor larvae meal inclusion affects hepatic proteome and apoptosis and/or autophagy of three farmed fish species

Herein, the effect of dietary inclusion of insect (Tenebrio molitor) meal on hepatic pathways of apoptosis and autophagy in three farmed fish species, gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and rainbow trout (Oncorhynchus mykiss), fed diets at 25%, 50% and 60% insect meal inclusion levels respectively, was investigated. Hepatic proteome was examined by liver protein profiles from the three fish species, obtained by two-dimensional gel electrophoresis. Although cellular stress was evident in the three teleost species following insect meal, inclusion by T. molitor, D. labrax and O. mykiss suppressed apoptosis through induction of hepatic autophagy, while in S. aurata both cellular procedures were activated. Protein abundance showed that a total of 30, 81 and 74 spots were altered significantly in seabream, European seabass and rainbow trout, respectively. Insect meal inclusion resulted in individual protein abundance changes, with less number of proteins altered in gilthead seabream compared to European seabass and rainbow trout. This is the first study demonstrating that insect meal in fish diets is causing changes in liver protein abundances. However, a species-specific response both in the above mentioned bioindicators, indicates the need to strategically manage fish meal replacement in fish diets per species

Ancestral absence of electron transport chains in Patescibacteria and DPANN

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., Onstott, T. C., Woyke, T., & Stepanauskas, R. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology, 11, (2020): 1848, doi:10.3389/fmicb.2020.01848.Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults

Interpreting diversity of proteobacteria based on 16S rrna gene copy number

The application of the 16S rRNA gene diversity analysis has revealed the immense microbial diversity of our planet. At the same time, and after of more than two decades of using this methodology along with several important improvements and new techniques, there is still no universal golden rule on how to estimate prokaryotic diversity in a natural sample, as there is in macroecology. A general assumption during studies of prokaryotic diversity is that each found 16S rRNA gene found corresponds to one cell. However, in this paper it is shown that recent genomic data reveal that this is not the case for several bacterial phyla. Since the Proteobacteria, along with the Firmicutes, are the most abundant and diverse bacterial phyla, in this paper the average 16S rRNA gene copy number is presented at the sub-phylum (α-, β-, γ-, δ- and ε-Proteobacteria), order and family level of the Proteobacteria phylum. At the sub-phylum level the average 16S rRNA gene copy number varied between 2.1±1.3 and 5.8±2.8. Since the 16S rRNA gene copy number affects the relative abundance of each proteobacterial species/phylotype found in a clone library, and subsequently the estimation of diversity, the corrected relative abundances of the found proteobacterial phylotypes were estimated in 37 clone libraries from six different natural habitats. It is suggested, that at least in the cases where Proteobacteria consist 50-75% of the clone library, the corrected abundances should be used for diversity estimations. © 2011 Nova Science Publishers, Inc. All rights reserved

Bacterioplankton growth on extracellular organic carbon from marine microalgal cultures

Marine bacterial growth on extracellular organic carbon (EOC) of Chlorella minutissima, Dimaliella tertiolecta and Chaetoceros gracilis was studied. EOC was retrieved after filtration of optimum growing algal cultures at the middle of the exponential growth phase and the stationary phase. The filtrates were inoculated with natural marine bacterial assemblages. The batch cultures were monitored for dissolved organic carbon (DOC) concentrations, bacterial yield, biomass and oxygen respiration over a period 3.5-10 days. The overall bacterial response was statistically different between the algal species origin of EOC and between the two growth phases for each species. These differences were also found for DOC normalised values suggesting that they were due to qualitative differences of the EOC. The highest bacterial yield was induced by the EOC originating from D. tertiolecta and the lowest by the C. minutissinia EOC. Oxygen respiration followed the same pattern with significantly higher values in the cultures with D. tertiolecta and C. gracilis stationary phase EOC. DOC degradation rate, utilisable DOC, bacterial growth rate and bacterial growth efficiency was different between the EOC from the exponential and stationary phase of algal growth, only in the case of C. gracilis. Of all the algal species studied here, it seems that the exponential C. gracilis EOC is more labile for marine bacteria

Interconnectivity vs. isolation of prokaryotic communities in European deep-sea mud volcanoes

During the past two decades, European cold seep ecosystems have attracted the scientific interest and to date there are several studies which have investigated the community structure and biodiversity of individual sites. In order to gain a better insight into the biology, biodiversity, and biogeography of seep-associated microbial communities along Europe's continental margins, a comparative approach was applied in the present work. By exploiting the publicly available data on 16S rRNA gene sequences retrieved from sediments of the Hakon Mosby mud volcano, Gulf of Cadiz and the eastern Mediterranean mud volcanoes/pockmarks (Anaximander area and Nile Fan), we investigated the prokaryotic biological components connecting these geographically isolated systems. The construction of interaction networks for both archaeal and bacterial shared operational taxonomic units (OTUs) among the different sites, revealed the presence of persistent OTUs, which can be considered as "key-players". One archaeal OTU (HQ588641) belonging to the ANME-3 group and one delta-Proteobacteria (HQ588562) were found in all five investigated areas. Other Archaea OTUs shared between four sites or less, belonged to the ANME-2c, -2a, MBG-D, -B and Thaumarchaeota. All other shared Bacteria belonged to the delta- and gamma-Proteobacteria, with the exception of one JS1 affiliate OTU. The distribution of the majority of the shared OTUs seems to be restricted in cold seeps, mud volcanoes and other marine methane-rich environments. Although the investigated sites were connected through a small number of OTUs, these microorganisms hold central ecophysiological roles in these sediments, namely methane-and sulfur-mediated mineralization

Cyanobacterial Toxin Degrading Bacteria: Who Are They?

Cyanobacteria are ubiquitous in nature and are both beneficial and detrimental to humans. Benefits include being food supplements and producing bioactive compounds, like antimicrobial and anticancer substances, while their detrimental effects are evident by toxin production, causing major ecological problems at the ecosystem level. To date, there are several ways to degrade or transform these toxins by chemical methods, while the biodegradation of these compounds is understudied. In this paper, we present a meta-analysis of the currently available 16S rRNA and mlrA (microcystinase) genes diversity of isolates known to degrade cyanobacterial toxins. The available data revealed that these bacteria belong primarily to the Proteobacteria, with several strains from the sphingomonads, and one from each of the Methylobacillus and Paucibacter genera. Other strains belonged to the genera Arthrobacter, Bacillus, and Lactobacillus. By combining the ecological knowledge on the distribution, abundance, and ecophysiology of the bacteria that cooccur with toxic cyanobacterial blooms and newly developed molecular approaches, it is possible not only to discover more strains with cyanobacterial toxin degradation abilities, but also to reveal the genes associated with the degradation of these toxins

Gut bacteria associated with different diets in reared Nephrops norvegicus

The impact of different diets on the gut microbiota of reared Nephrops norvegicus was investigated based on bacterial 16S rRNA gene diversity. Specimens were collected from Pagasitikos Gulf (Greece) and kept in experimental rearing tanks, under in situ conditions, for 6 months. Treatments included three diets: frozen natural (mussel) food (M), dry formulated pellet (P) and starvation (S). Gut samples were collected at the initiation of the experiment, and after 3 and 6 months. Tank water and diet samples were also analyzed for bacterial 16S rRNA gene diversity. Statistical analysis separated the two groups fed or starved (M and P vs. S samples). Most gut bacteria were not related to the water or diet bacteria, while bacterial diversity was higher in the starvation samples. M and P samples were dominated by Gammaproteobacteria, Epsilonproteobacteria and Tenericutes. Phylotypes clustering in Photobacterium leiognathi, Shewanella sp. and Entomoplasmatales had high frequencies in the M and P samples but low sequence frequencies in S samples. The study showed that feeding resulted in the selection of specific species, which also occurs in the natural population, and might be associated with the animal's nutrition. (C) 2012 Elsevier GmbH. All rights reserved

Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site (9 degrees N, East Pacific Rise)

A diffusely venting chimney spire from the East Pacific Rise (9 degrees N) was analysed by petrographic thin sectioning and 16S rRNA gene cloning and sequencing in parallel, to correlate microbial community composition with mineralogy and inferred in situ conditions within the chimney mineral matrix. Both approaches indicated a zonation of the chimney spire into distinct microhabitats for different bacteria and archaea. The thermal gradient inferred from the mineral composition and porosity of the chimney was consistent with the distribution of bacterial and archaeal phylotypes in the chimney matrix. A novel phylogenetic lineage of euryarchaeota was found that co-occurred with clones related to cultured hyperthermophilic archaea. A few phylotypes related to mesophilic bacteria were found in the hot core of the chimney, indicating that seawater influx during retrieval and cooling of these highly porous structures can entrain microorganisms into chimney layers that are not their native habitat