"Candidatus Colwellia aromaticivorans" sp. nov., "Candidatus Halocyntiibacter alkanivorans" sp. nov., and "Candidatus Ulvibacter alkanivorans" sp. nov. Genome Sequences

Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance

Random forests have emerged as a promising tool in comparative metagenomics because they can predict environmental characteristics based on microbial composition in datasets where β-diversity metrics fall short of revealing meaningful relationships between samples. Nevertheless, despite this efficacy, they lack biological insight in tandem with their predictions, potentially hindering scientific advancement. To overcome this limitation, we leverage a geometric characterization of random forests to introduce a data-driven phylogenetic β-diversity metric, the adaptive Haar-like distance. This new metric assigns a weight to each internal node (i.e., split or bifurcation) of a reference phylogeny, indicating the relative importance of that node in discerning environmental samples based on their microbial composition. Alongside this, a weighted nearest-neighbors classifier, constructed using the adaptive metric, can be used as a proxy for the random forest while maintaining accuracy on par with that of the original forest and another state-of-the-art classifier, CoDaCoRe. As shown in datasets from diverse microbial environments, however, the new metric and classifier significantly enhance the biological interpretability and visualization of high-dimensional metagenomic samples.

Halocynthiibacter halioticoli sp. nov., isolated from the viscera of abalone Haliotis discus hannai

A Gram-stain-negative, rod-shaped, glide, non-flagellated, and facultatively anaerobic bacterial strain, designated as Z654T, was isolated from the gut of abalone Haliotis discus hannai from Rongcheng, Shandong province, China. Cells are 0.2-0.8 μm in width and 0.7-3.4 μm in length. Cells grew best at 30 °C (range, 15-37 °C), pH 7.0 (range, 6.0-8.5) and NaCl concentration of 2.0% (w/v) (range, 1-10%). According to the phylogenetic analysis of 16S rRNA gene sequence, the strain belongs to the genus Halocynthiibacter and the closest strain is Halocynthiibacter arcticus KCTC 42129 T (97.12%). The genome size of strain Z654T was 3,296,250 bp and the DNA G + C content was 54.2 mol%. The average nucleotide identity (ANI) scores and digital DNA-DNA hybridization (dDDH) scores with H. arcticus KCTC 42129 T were 70% and 14.6-18.2%, respectively. The predominant quinone was Q-10 and the major fatty acids were C18:0, C18:1 ω7c 11-methyl and summed feature 8. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid and unidentifed lipids. Based on the phenotypic, phylogenetic and chemotaxonomic data, strain Z654T was considered to represent a novel species of the genus Halocynthiibacter, for which the name Halocynthiibacte halioticoli sp. nov., is proposed. The type strain is Z654T (= MCCC 1H00503T = KCTC 92003 T).

Abundance and diversity of n-alkane and PAH-degrading bacteria and their functional genes - Potential for use in detection of marine oil pollution

Monitoring environmental status through molecular investigation of microorganisms in the marine environment is suggested as a potentially very effective method for biomonitoring, with great potential for automation. There are several hurdles to that approach with regards to primer design, variability across geographical locations, seasons, and type of environmental pollution. Here, qPCR analysis of genes involved in the initial activation of aliphatic and aromatic hydrocarbons were used in a laboratory setup mimicking realistic oil leakage at sea. Seawater incubation experiments were carried out under two different seasons with two different oil types. Degenerate primers targeting initial oxygenases (alkane 1-monooxygenase; alkB and aromatic-ring hydroxylating dioxygenase; ARHD) were employed in qPCR assays to quantify the abundance of genes essential for oil degradation. Shotgun metagenomics was used to map the overall community dynamics and the diversity of alkB and ARHD genes represented in the microbial community. The amplicons generated through the qPCR assays were sequenced to reveal the diversity of oil-degradation related genes captured by the degenerate primers. We identified a major mismatch between the taxonomic diversity of alkB and ARHD genes amplified by the degenerate primers and those identified through shotgun metagenomics. More specifically, the designed primers did not amplify the alkB genes of the two most abundant alkane degraders that bloomed in the experiments, Oceanobacter and Oleispira. The relative abundance of alkB sequences from shotgun metagenomics and 16S rRNA-based Oleispira-specific qPCR assay were better signals for oil in water than the tested qPCR alkB assay. The ARHD assay showed a good agreement with PAHs degradation despite covering only 25% of the top 100 ARHD genes and missing several abundant Cycloclasticus sequences that were present in the metagenome. We conclude that further improvement of the degenerate primer approach is needed to rely on the use of oxygenase-related qPCR assays for oil leakage detection.

Biodegradation of water-accommodated aromatic oil compounds in Arctic seawater at 0 °C

Oil spills in Arctic marine environments are expected to increase concurrently with the expansion of shipping routes and petroleum exploitation into previously inaccessible ice-dominated regions. Most research on oil biodegradation focusses on the bulk oil, but the fate of the water-accommodated fraction (WAF), mainly composed of toxic aromatic compounds, is largely underexplored. To evaluate the bacterial degradation capacity of such dissolved aromatics in Greenlandic seawater, microcosms consisting of 0 °C seawater polluted with WAF were investigated over a 3-month period. With a half-life (t_1/2) of 26 days, m-xylene was the fastest degraded compound, as measured by gas chromatography - mass spectrometry. Substantial slower degradation was observed for ethylbenzene, naphthalenes, phenanthrene, acenaphthylene, acenaphthene and fluorenes with t_1/2 of 40-105 days. Colwellia, identified by 16S rRNA gene sequencing, was the main potential degrader of m-xylene. This genus occupied up to 47 % of the bacterial community until day 10 in the microcosms. Cycloclasticus and Zhongshania aliphaticivorans, potentially utilizing one-to three-ringed aromatics, replaced Colwellia between day 10 and 96 and occupied up to 6 % and 23 % of the community, respectively. Although most of the WAF can ultimately be eliminated in microcosms, our results suggest that the restoration of an oil-impacted Arctic environment may be slow as most analysed compounds had t_1/2 of over 2-3 months and the detrimental effects of a spill towards the marine ecosystem likely persist during this time.

Startup of pilot-scale single-stage nitrogen removal using anammox and partial nitritation (SNAP) reactor for waste brine treatment using marine anammox bacteria

This study is the first to demonstrate the startup of a pilot-scale single-stage nitrogen removal using anammox and partial nitritation (SNAP) reactor utilizing marine anammox bacteria. A complete mixing type reactor, continuously fed with waste brine obtained from a natural gas plant (salinity 3%, NH₄⁺-N 130-180 mg/L) and having an effective volume of 2 m³, achieved stable operation at temperatures of 20-30°C with a maximum nitrogen removal rate of 1.43 kg-N/m³/day. During the startup process, along with a small amount of seed sludge, granular sludge was additionally inoculated as a biomass carrier for the enrichment of ammonia oxidizing bacteria (AOB), followed by the enrichment of anammox bacteria. A mesh screen equipped at the outlet of the reactor facilitated the successful sludge retention in the reactor. Analysis of bacterial community composition indicated that Candidatus Scalindua was successfully enriched in the pilot SNAP reactor. These methods for stable sludge retention in the reactor greatly contributed to the startup of the first pilot-scale SNAP reactor using marine anammox bacteria.

A highly conserved mechanism for the detoxification and assimilation of the toxic phytoproduct L-azetidine-2-carboxylic acid in Aspergillus nidulans

Plants produce toxic secondary metabolites as defense mechanisms against phytopathogenic microorganisms and predators. L-azetidine-2-carboxylic acid (AZC), a toxic proline analogue produced by members of the Liliaceae and Agavaciae families, is part of such a mechanism. AZC causes a broad range of toxic, inflammatory and degenerative abnormalities in human and animal cells, while it is known that some microorganisms have evolved specialized strategies for AZC resistance. However, the mechanisms underlying these processes are poorly understood. Here, we identify a widespread mechanism for AZC resistance in fungi. We show that the filamentous ascomycete Aspergillus nidulans is able to not only resist AZC toxicity but also utilize it as a nitrogen source via GABA catabolism and the action of the AzhA hydrolase, a member of a large superfamily of detoxifying enzymes, the haloacid dehalogenase-like hydrolase (HAD) superfamily. This detoxification process is further assisted by the NgnA acetyltransferase, orthologue of Mpr1 of Saccharomyces cerevisiae. We additionally show that heterologous expression of AzhA protein can complement the AZC sensitivity of S. cerevisiae. Furthermore, a detailed phylogenetic analysis of AzhA homologues in Fungi, Archaea and Bacteria is provided. Overall, our results unravel a widespread mechanism for AZC resistance among microorganisms, including important human and plant pathogens.

Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort

The marine bone biome is a complex assemblage of macro- and microorganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia IMPORTANCE Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment. We here demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Metatranscriptomic Analysis of Oil-Exposed Seawater Bacterial Communities Archived by an Environmental Sample Processor (ESP)

The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, Day 4 and Day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ring-degrading enzymes (e.g., ben, box, and dmp clusters) were observed on Day 4 in both control and oil-exposed and non-exposed tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus were significantly enriched in the oil-treated exposed tank in comparison to control the non-exposed tank, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.