The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea

Introduction

The geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme-and unique-oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described.

Methods

To test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria.

Results and discussion

This approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536^T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536^T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.

Sinomicrobium kalidii sp. nov., an indole-3-acetic acid-producing endophyte from a shoot of halophyte Kalidium cuspidatum

To better understand the effects of endophytic bacteria on halophytes, a bacteria that produced indole-3-acetic acid and 1-aminocyclopropane-1-carboxylic acid deaminase, designated HD2P242^T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. The cells of strain HD2P242^T were Gram-stain-negative, strictly aerobic, motile by gliding, non-spore-forming and rod-shaped. Strain HD2P242^T grew at pH 6.0-9.0 (optimum, pH 7.0) and 10-45 °C (optimum 37 °C), in the presence of 0-8 % (w/v) NaCl (optimum, 4 %). The strain was positive for oxidase and catalase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both showed that strain HD2P242^T clustered with Sinomicrobium pectinilyticum 5DNS001^T and S. oceani SCSIO 03483^T, and had 95.6, 94.3 and <94.3 % 16S rRNA gene similarities to S. pectinilyticum 5DNS001^T, S. oceani SCSIO 03483^T and all the other current type strains. Strain HD2P242^T contained menaquinone 6 as its sole respiratory quinone. Its major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids were iso-C_17 : 0, iso-C_16 : 0 3-OH, anteiso-C_17 : 0 and summed feature 6 (C_19 : 1  ω9c and/or C_19 : 1  ω11c). The genome consisted of a 5 364 211 bp circular chromosome, with a G+C content of 45.1 mol%, predicting 4391 coding sequence genes, 47 tRNA genes and two rRNA operons. The average nucleotide identity based on blast and the digital DNA-DNA hybridization values of strain HD2P242^T with S. oceani SCSIO 03483^T and S. pectinilyticum 5DNS001^T were 73.8 and 77.0%, and 22.3 and 22.2%, respectively. The comparative genome analysis showed that the pan-genomes of strain HD2P242^T and three Sinomicrobium type strains possessed 4236 clusters, whereas the core genome possessed 2162 clusters, which accounted for 52.3 % of all the clusters. The genomic analysis revealed that all four Sinomicrobium members could utilize d-glucose by the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway. The tricarboxylic acid cycle was utilized as a metabolic centre. The phylogenetic, physiological and phenotypic characteristics allowed the discrimination of strain HD2P242^T from its phylogenetic relatives. Therefore, Sinomicrobium kalidii sp. nov. is proposed, and the type strain is HD2P242^T (=CGMCC 1.19025^T=KCTC 92136^T).

Sinomicrobium weinanense sp. nov., a halophilic bacterium isolated from saline-alkali soil

A Gram-stain-negative, facultative anaerobic, non-motile, rod-shaped strain was isolated from saline-alkali soil collected in PR China, and it was designated as strain FJxs T . Its optimal growth was observed at 37–40 °C in the presence of 0–3 % (w/v) NaCl (pH 7.0). The major fatty acids of strain FJxs T were iso-C15 : 0, iso-C17 : 0 3OH, summed feature 3, C16 : 0 and iso-C15 : 1 G. The predominant respiratory quinone was menaquinone 6. The DNA G+C content of the strain was 45.18 mol%. Whole genome and 16S rRNA gene sequence analyses indicated that strain FJxs T exhibited 94.78 % sequence identity (the maximum) with Sinomicrobium soli N-1-3-6T, 94.36 % with Sinomicrobium pectinilyticum 5DNS001T, and 93.52 % with Sinomicrobium oceani SCSIO 03483T. Analyses of genotypic, phenotypic, phylogenetic and chemotaxonomic characteristics indicated that strain FJxs T represented a novel species of the genus Sinomicrobium . This novel species was named Sinomicrobium weinanense sp. nov. with its type strain as FJxs T (=CCTCC AB 2019251T=KCTC 72740T).

Sinomicrobium soli sp. nov., isolated from arctic soil

A bacterial strain, designated N-1-3-6T, was isolated from a soil sample collected from the arctic regions. The cells were short rods, Gram-stain-negative, catalase- and oxidase-positive. Growth was observed with 0–12 % (w/v) NaCl, with optimal growth at 0.5–2 %, and at pH 6.0–9.0, with optimum of pH 7.0, and a growth temperature of 10–45 °C, with an optimum of 28–37 °C. Phylogenetic analysis based on the 16S rRNA gene placed N-1-3-6T in the genus Sinomicrobium with the closest relative being Sinomicrobium pectinilyticum 5DNS001T, exhibiting 95.3 % 16S rRNA pairwise similarity. A polyphasic taxonomic study, including phenotypic, chemotaxonomic and molecular analyses, was performed to clarify its taxonomic position. N-1-3-6T contained MK-6 as the predominant menaquinone. Polar lipids consisted of phosphatidylethanolamine and several unidentified aminolipids, phospholipids and lipids. The principal fatty acids (>10 %) were iso-C15 : 0 (26.9 %), summed feature 3 [C16 : ω7c/ω6c (17.2 %)] and iso-C17 : 0 3-OH (14.7 %). The DNA G+C content of N-1-3-6T was 47.7 mol%. On the basis of its phenotypic and genotypic properties, strain N-1-3-6T should be classified as representing a novel species of the genus Sinomicrobium , for which the name Sinomicrobium soli sp. nov. is proposed, with the type strain N-1-3-6T (=MCCC 1A06047T=KCTC 52339T).