Biology subjects

Kouris, A.

Publications and source records attributed to Kouris, A..

6 recordsLinked to original sources

bioRxiv2023

High diversity, abundance and expression of hydrogenases in groundwater

Hydrogen may be the most important electron donor available in the subsurface. Here we analyze the diversity, abundance and expression of hydrogenases in 5 proteomes, 25 metagenomes and 265 amplicon datasets of groundwaters with diverse geochemistry. A total of 1,772 new [NiFe]-hydrogenase gene sequences were recovered, which almost doubled the number of sequences in a widely used database. [NiFe]-hydrogenases were highly abundant, almost as abundant as the DNA-directed RNA polymerase. The abundance of hydrogenase genes increased with depth from 0 to 129 m. Hydrogenases were present in 502 out of 1,245 metagenome-assembled-genomes. The populations with hydrogenases accounted for [~]50% of all populations. Hydrogenases were actively expressed, making up as much as 5.9% of methanogen proteomes. Most of the newly discovered diversity of hydrogenases was in "Group 3b", which was linked to sulfur metabolism. "Group 3d" was the most abundant, which was previously linked to fermentation, but we observed this group mainly in methanotrophs and chemoautotrophs. "Group 3a", associated with methanogenesis, was the most active in proteomes. Two newly discovered groups of [NiFe]-hydrogenases further expanded the biodiversity. Our results highlight the vast diversity, abundance and expression of hydrogenases in the sampled groundwaters, suggesting a high potential for hydrogen oxidation in subsurface habitats.

microbiology↗

bioRxiv2022

A naturally occurring lytic bioprocess improves sustainability of phycocyanin production from cyanobacteria

Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover, supplementing heightened heterotrophic respiration and oxygen drawdown. Here we use metagenomics and metaproteomics to survey the cellular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for visral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating involvement in the programmed cell death response. We propose this natural form of programmed cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.

microbiology↗

bioRxiv2022

Frequency of change determines effectiveness of microbial response strategies in sulfidic stream microbiomes

Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the ecological success of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1 day, 4 days and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved 26 nearly complete genomes of bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Apparently, oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. Rapid (1-day) dynamics yielded more stochasticity, both in community dynamics and gene expression, indicating that bet-hedging might be an effective coping strategy for relatively rapid environmental change. Codon-usage bias, previously associated with copiotrophic and oligotrophic lifestyles, was found to be a powerful predictor of ecological success at different frequencies, with copiotrophs and oligotrophs more successful at a rapid and a slow pace of change, respectively, independent of growth rate.

microbiology↗

bioRxiv2021

Ultra-sensitive Protein-SIP to quantify activity and substrate uptake in microbiomes with stable isotopes

Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS, are limited in terms of sensitivity, resolution or throughput. Here we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by [~]90% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. It allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics LC-MS/MS measurements. The analysis has been implemented as an open-source application (https://sourceforge.net/projects/calis-p/). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber based prebiotics. In summary, we demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01% to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

microbiology↗

bioRxiv2019

Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation

Since the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic fixation of CO2 by the symbionts drives these nutritional associations. In this study, we investigated Candidatus Kentron, the clade of symbionts hosted by Kentrophoros, a diverse genus of ciliates which are found in marine coastal sediments around the world. Despite being the main food source for their hosts, Kentron lack the key canonical genes for any of the known pathways for autotrophic fixation, and have a carbon stable isotope fingerprint unlike other thiotrophic symbionts from similar habitats. Our genomic and transcriptomic analyses instead found metabolic features consistent with growth on organic carbon, especially organic and amino acids, for which they have abundant uptake transporters. All known thiotrophic symbionts have converged on using reduced sulfur to generate energy lithotrophically, but they are diverse in their carbon sources. Some clades are obligate autotrophs, while many are mixotrophs that can supplement autotrophic carbon fixation with heterotrophic capabilities similar to those in Kentron. We have shown that Kentron are the only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other thiotrophic symbionts studied to date, which possess either the Calvin-Benson-Bassham or reverse tricarboxylic acid cycles for autotrophy. Significance StatementMany animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO2, serving as primary producers for their hosts. Here we describe apparently non-autotrophic sulfur symbionts called Kentron, associated with marine ciliates. They lack genes for known autotrophic pathways, and have a carbon stable isotope fingerprint heavier than other symbionts from similar habitats. Instead they have the potential to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a metabolic mode called chemolithoheterotrophy that is not found in other symbioses. Although several symbionts have heterotrophic features to supplement primary production, in Kentron they appear to supplant it entirely.

microbiology↗

bioRxiv2018

VarSome: The Human Genomic Variant SearchEngine

SummaryVarSome.com is a search engine, aggregator and impact analysis tool for human genetic variation and a community-driven project aiming at sharing global expertise on human variants.\n\nAvailabilityVarSome is freely available at http://varsome.com.

bioinformatics↗