Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.

While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA. IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.

Foliar N2 O emissions constitute a significant source to atmosphere.

Nitrous oxide (N2 O) is a potent greenhouse gas and causes stratospheric ozone depletion. While the emissions of N2 O from soil are widely recognized, recent research has shown that terrestrial plants may also emit N2 O from their leaves under controlled laboratory conditions. However, it is unclear whether foliar N2 O emissions are universal across varying plant taxa, what the global significance of foliar N2 O emissions is, and how the foliage produces N2 O in situ. Here we investigated the abilities of 25 common plant taxa, including trees, shrubs and herbs, to emit N2 O under in situ conditions. Using 15 N isotopic labeling, we demonstrated that the foliage-emitted N2 O was predominantly derived from nitrate. Moreover, by selectively injecting biocide in conjunction with the isolating and back-inoculating of endophytes, we demonstrated that the foliar N2 O emissions were driven by endophytic bacteria. The seasonal N2 O emission rates ranged from 3.2 to 9.2 ng N2 O-N g-1 dried foliage h-1 . Extrapolating these emission rates to global foliar biomass and plant N uptake, we estimated global foliar N2 O emission to be 1.21 and 1.01 Tg N2 O-N year-1 , respectively. These estimates account for 6%-7% of the current global annual N2 O emission of 17 Tg N2 O-N year-1 , indicating that in situ foliar N2 O emission is a universal process for terrestrial plants and contributes significantly to the global N2 O inventory. This finding highlights the importance of measuring foliar N2 O emissions in future studies to enable the accurate assigning of mechanisms and the development of effective mitigation.

Community assembly of organisms regulates soil microbial functional potential through dual mechanisms.

Unraveling the influence of community assembly processes on soil ecosystem functioning presents a major challenge in the field of theoretical ecology, as it has received limited attention. Here, we used a series of long-term experiments spanning over 25 years to explore the assembly processes of bacterial, fungal, protist, and nematode communities using high-throughput sequencing. We characterized the soil microbial functional potential by the abundance of microbial genes associated with carbon, nitrogen, phosphorus, and sulfur cycling using GeoChip-based functional gene profiling, and determined how the assembly processes of organism groups regulate soil microbial functional potential through community diversity and network stability. Our results indicated that balanced fertilization (NPK) treatment improved the stochastic assembly of bacterial, fungal, and protist communities compared to phosphorus-deficient fertilization (NK) treatment. However, there was a nonsignificant increase in the normalized stochasticity ratio of the nematode community in response to fertilization across sites. Our findings emphasized that soil environmental factors influenced the assembly processes of the biotic community, which regulated soil microbial functional potential through dual mechanisms. One mechanism indicated that the high phosphorus levels and low soil nutrient stoichiometry may increase the stochasticity of bacterial, fungal, and protist communities and the determinism of the nematode community under NPK treatment, ultimately enhancing soil microbial functional potential by reinforcing the network stability of the biotic community. The other mechanism indicated that the low phosphorus levels and high soil nutrient stoichiometry may increase the stochastic process of the bacterial community and the determinism of the fungal, protist, and nematode communities under NK treatment, thereby enhancing soil microbial functional potential by improving the ß-diversity of the biotic community. Taken together, these results provide valuable insights into the mechanisms underlying the assembly processes of the biotic community that regulate ecosystem functioning.

Crenobacter oryzisoli sp. nov., a novel phosphate-solubilizing bacterium isolated from the paddy soil.

Two Gram-staining-negative, facultative anaerobic, rod-shaped and phosphate-solubilizing strains designated SG2303T and SG2305, were isolated from paddy soil in China. Phylogenetic analysis based on 16 S rRNA gene sequences indicated that SG2303T and SG2305 represented a member of the genus Crenobacter within the family Neisseriaceae of the phylum Pseudomonadota. Strain SG2303T displayed higher 16 S rRNA gene sequence similarities with members of the genus Crenobacter ranging from 93.5 to 94.0%. Strains C. luteus YIM 78141T and C. cavernae K1W11S-77T were closest related to the isolated strains and were considered as type strains. Growth of strain SG2303T occurred at 10-55 °C (optimum 37 °C), pH 5.0-9.0 (optimum pH 6.0-7.0) and 0-1% (w/v) NaCl (optimum 0%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG2303T and its closely related taxa were 76.1-78.2% and 20.5-22.1%, respectively. The genomic DNA G + C content was 62.2%. The quinone of strain SG2303T was Q-8. The major fatty acids (> 10%) of strain SG2303T were C16:0 (30.6%), summed feature 3 (C16:1ω7c and/or C16:1ω6c) (26.0%) and C12:0 3OH (12.1%). The polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phospholipids (PL), glycolipid (GL) and unidentified lipids (UL). Based on the results of the phylogenetic, physiological, biochemical, and morphological analysis, strain SG2303T is recognized as a novel species of the genus Crenobacter, for which the name Crenobacter oryzisoli sp. nov. is proposed. The type strain is SG2303T (= GDMCC 1.3970T = JCM 36468T). In addition, SG2303T was also able of phosphorus solubilization and promoting the growth of rice seeds. Strain SG2303T exhibited a relatively high dissolvable phosphorus content of 2.52 µg·mL- 1.

Three Fe(III)-reducing and nitrogen-fixing bacteria, Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., isolated from paddy soil.

Three microaerophilic bacterial strains, designated SG22T, SG63T and SG29T were isolated from paddy soils in PR China. Cells of these strains were Gram-staining-negative and long rod-shaped. SG22T, SG63T and SG29T showed the highest 16S rRNA gene sequence similarities with the members of the genus Anaeromyxobacter. The results of phylogenetic and phylogenomic analysis also indicated that these strains clustered with members of the genus Anaeromyxobacter. The main respiratory menaquinone of SG22T, SG63T and SG29T was MK-8 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. SG22T, SG29T and SG63T not only possessed iron reduction ability but also harboured genes (nifHDK) encoding nitrogenase. The genomic DNA G+C contents of SG22T, SG63T and SG29T ranged from 73.3 to 73.5 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between SG22T, SG63T and SG29T and the closely related species of the genus Anaeromyxobacter were lower than the cut-off values (dDDH 70 % and ANI 95-96 %) for prokaryotic species delineation. On the basis of these results, strains SG22T, SG63T and SG29T represent three novel species within the genus Anaeromyxobacter, for which the names Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., are proposed. The type strains are SG22T (= GDMCC 1.3185T = JCM 35581T), SG63T (= GDMCC 1.2914T = JCM 35124T) and SG29T (= GDMCC 1.2911T = JCM 35123T).

Natural AIEgens as Ultraviolet Sunscreens and Photosynergists for Solar Fuel Production.

Bio-nano hybrids (BNH), combining semiconductors and microorganisms, have shown great promise for effective solar-to-fuel energy conversion. However, the high-energy ultraviolet (UV) photons in the solar spectrum can cause severe photocorrosion of semiconductors and irreversible photodamage to microorganisms within BNH. Here, we developed an encapsulation strategy using natural luminogens with aggregation-induced emission characteristics (AIEgens) to construct a protective layer for BNH, effectively shielding them against high-energy UV photons. We incorporated natural berberine (BBR) into the BNH composed of Methanosarcina barkeri and polymeric carbon nitrides (CNx). The self-assembled BNH-BBR system displayed a 2.75-fold higher CH4 yield than BNH under simulated solar irradiation. Mechanism analysis revealed that BBR acted as a UV sunscreen for BNH by converting high-energy short wavelengths into low-energy long wavelengths, thereby reducing the accumulation of reactive oxygen species and alleviating the photocorrosion of CNx. Furthermore, BBR functioned as a photosynergist for BNH by regulating photoelectron production and utilization, enhancing the intracellular energy formation in M. barkeri for growth and metabolism. This work provides important insights into the effective and scalable conversion of CO2 into valuable biofuels with BNH under light illumination containing high-energy photons.

Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils.

In this research, two novel Fe(III)-reducing bacteria, SG10T and SG198T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10T and SG198T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10T and SG198T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189T (99.0-99.5%) and Geothrix paludis SG195T (99.0-99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10T and SG198T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1-94.3% and 30.7-59.5%, respectively. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:0 and iso-C13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10T (= GDMCC 1.3406 T = JCM 39331 T) and SG198T (= GDMCC 62910 T = KCTC 25635 T), respectively.

Genome-based taxonomy and functional prediction of Sphingomonas fuzhouensis sp. nov. and Massilia phyllosphaerae sp. nov. isolated from Pennisetum sp. with plant growth-promoting potential.

Two facultatively aerobic strains, designated SGZ-02T and SGZ-792T, were isolated from plant Pennisetum sp., exhibiting the highest 16S rRNA gene sequence similarities with the type strains of Sphingomonas zeae LMG 28739T (98.6%) and Massilia forsythiae NBRC 114511T (98.4%), respectively. SGZ-02T grew between 5 and 45 °C, pH 5.0-11.0 and tolerated NaCl concentrations of 0-4% (w/v), whereas SGZ-792T thrived at 5-40 °C, pH 5.0-11.0 and NaCl tolerance to 0-3.5% (w/v). The major quinone of SGZ-02T was ubiquinone-10, with the dominant fatty acids being C16:0 (13.5%), Summed Feature 3 (6.3%), C14:02-OH (5.3%) and Summed Feature 8 (66.3%). SGZ-792T predominantly contained ubiquinone-8, with major fatty acids being C16:0 (20.3%), Summed Feature 3 (5.0%) and Summed Feature 8 (54.7%). Average nucleotide identity and digital DNA-DNA hybridization values between two strains and their closest references strains were below the bacterial species threshold. Based on genotypic and phenotypic characteristics, strains SGZ-02T and SGZ-792T are proposed as novel species within the genera Sphingomonas and Massilia, respectively. The suggested names for the new species are Sphingomonas fuzhouensis sp. nov. (SGZ-02T = GDMCC 1.4033T = JCM 36769T) and Massilia phyllosphaerae sp. nov. (SGZ-792T = GDMCC 1.4211T = JCM 36643T), respectively.

Azotosporobacter soli gen. nov., sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.

A nitrogen-fixing strain designated SG130T was isolated from paddy soil in Fujian Province, China. Strain SG130T was Gram-staining-negative, rod-shaped, and strictly anaerobic. Strain SG130T showed the highest 16S rRNA gene sequence similarities with the type strains Dendrosporobacter quercicolus DSM 1736T (91.7%), Anaeroarcus burkinensis DSM 6283T (91.0%) and Anaerospora hongkongensis HKU 15T (90.9%). Furthermore, the phylogenetic and phylogenomic analysis also suggested strain SG130T clustered with members of the family Sporomusaceae and was distinguished from other genera within this family. Growth of strain SG130T was observed at 25-45 °C (optimum 30 °C), pH 6.0-9.5 (optimum 7.0) and 0-1% (w/v) NaCl (optimum 0.1%). The quinones were Q-8 and Q-9. The polar lipids were phosphatidylserine (PS), phosphatidylethanolamine (PE), glycolipid (GL), phospholipid (PL) and an unidentified lipid (UL). The major fatty acids (> 10%) were iso-C13:0 3OH (26.6%), iso-C17:1 (15.6%) and iso-C15:1 F (11.4%). The genomic DNA G + C content was 50.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T (ANI 68.0% and dDDH 20.3%) were both below the cut-off level for species delineation. The average amino acid identity (AAI) between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T was 63.2%, which was below the cut-off value for bacterial genus delineation (65%). Strain SG130T possessed core genes (nifHDK) involved in nitrogen fixation, and nitrogenase activity (106.38 µmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the above results, strain SG130T is confirmed to represent a novel genus of the family Sporomusaceae, for which the name Azotosporobacter soli gen. nov., sp. nov. is proposed. The type strain is SG130T (= GDMCC 1.3312T = JCM 35641T).

Abiotic Methane Production Driven by Ubiquitous Non-Fenton-Type Reactive Oxygen Species.

Abiotic CH4 production driven by Fenton-type reactive oxygen species (ROS) has been confirmed to be an indispensable component of the atmospheric CH4 budget. While the chemical reactions independent of Fenton chemistry to ROS are ubiquitous in nature, it remains unknown whether the produced ROS can drive abiotic CH4 production. Here, we first demonstrated the abiotic CH4 production at the soil-water interface under illumination. Leveraging this finding, polymeric carbon nitrides (CNx) as a typical analogue of natural geobattery material and dimethyl sulfoxide (DMSO) as a natural methyl donor were used to unravel the underlying mechanisms. We revealed that the ROS, photocatalytically produced by CNx, can oxidize DMSO into CH4 with a high selectivity of 91.5 %. Such an abiotic CH4 production process was further expanded to various non-Fenton-type reaction systems, such as electrocatalysis, pyrocatalysis and sonocatalysis. This work provides insights into the geochemical cycle of abiotic CH4, and offers a new route to CH4 production via integrated energy development.

Shouchella tritolerans sp. nov., a facultative anaerobic bacterium isolated from marine sediments.

An alkali, salt, and thermo-tolerant strain designated FJAT-45399T was isolated from marine sediment in Fujian Province, China. Strain FJAT-45399T was Gram-stain-positive, rod-shaped, and facultatively aerobic. It shared high 16S rRNA gene sequence similarities with the members of the genus Shouchella. Further, the phylogenetic and phylogenomic analysis also suggested strain FJAT-45399T clustered with the members of the genus Shouchella. Growth of strain FJAT-45399T was observed at 15-55 °C (optimum 45-50 °C), pH 7.0-13.0 (optimum 9.0) and 0-15% (w/v) NaCl (optimum 2%). It contained MK-7 as the menaquinone. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and an unidentified glycolipid (UGL) and lipid (UL). The major fatty acids (> 10%) were C16:0 (22.8%), iso-C15:0 (21.3%), and anteiso-C15:0 (14.0%). The genomic DNA G + C content was 44.5%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain FJAT-45399T and the most closely related type strain Shouchella clausii DSM 8716T (ANI 94.1% and dDDH 55.4%) were both below the cut-off level for species delineation. Based on the above results, strain FJAT-45399T represents a novel species of the genus Shouchella, for which the name Shouchella tritolerans sp. nov., is proposed. The type strain is FJAT-45399T (= GDMCC 1.3098T = JCM 35613T).

A novel sulfate-reducing and nitrogen-fixing bacterium Fundidesulfovibrio soli sp. nov., isolated from paddy soils.

A strictly anaerobic sulfate-reducing strain, designated SG60T, was isolated from paddy soil collected in Fujian Province, China. Growth of strain SG60T was observed at 20-37 °C, pH 5.5-10.0 and 0-0.7% (w/v) NaCl. Strain SG60T showed the highest 16S rRNA sequence similarities to the type strains of Fundidesulfovibrio magnetotacticus FSS-1T (97.2%) and Fundidesulfovibrio putealis DSM 16056T (96.4%). Phylogenetic trees based on the16S rRNA sequence and genome-based phylogenomic tree constructed using 120 core genes showed that strain SG60T clustered with members of the genus Fundidesulfovibrio. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG60T and the most closely related type strain F. magnetotacticus were 78.2% and 21.6%, respectively. Strain SG60T contained MK-7 as the main respiratory quinone and anteiso-C15:0, anteiso-C17:1 ω9c, iso-C16:0 and iso-C16:1 H as the major fatty acids. Strain SG60T produced desulfoviridin and possessed genes (nifHDK) encoding functions involved in nitrogen fixation. The genomic DNA G + C content was 65.5%. Based on the observed physiological properties, chemotaxonomic characteristics and ANI and dDDH values, strain SG60T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio soli sp. nov. is proposed. The type strain is SG60T (= GDMCC 1.3310T = JCM 35676T).

A novel nitrogen-fixing bacterium, Propionivibrio soli sp. nov. isolated from paddy soil.

A facultative anaerobic nitrogen-fixing bacterium, designated SG131T, was isolated from paddy soil. Strain SG131T showed high 16S rRNA gene sequence similarities with type strains Propionivibrio limicola DSM 6832T (96.9%), Propionivibrio pelophilus asp 66T (96.0%) and Propionivibrio dicarboxylicus DSM 5885T (95.7%). The phylogenetic trees (based on 16S rRNA gene sequences and 120 conserved genes from genomes, respectively) indicated that strain SG131T clustered with members of the genus Propionivibrio. Growth of strain SG131T was observed at 25-40 °C, pH 5.5-10.5 and 0-0.5% (w/v) NaCl. The quinone was Q-7, and the main fatty acids were C16:1 ω6c and/or C16:1 ω7c (25.9%), C16:0 (23.3%), C17:0-cyclo (11.7%), C12:0 (6.0%) and C17:0 (5.9%). The genomic DNA G + C content of strain SG131T was 60.3%. The average nucleotide identity (ANI) values between strain SG131T and its most closely related species P. limicola DSM 6832T, P. pelophilus DSM 12018T and P. dicarboxylicus DSM 5885T were 74.4%, 74.9% and 75.6%, respectively. The digital DNA-DNA hybridization (dDDH) values between strain SG131T and its most closely related species P. limicola DSM 6832T, P. pelophilus DSM 12018T and P. dicarboxylicus DSM 5885T were 19.9%, 20.6% and 20.5%, respectively. All these values were lower than the recommended species delineation thresholds of ANI (95-96%) and dDDH (70%). Strain SG131T possessed core genes (nifHDK) of nitrogen fixation and was confirmed its nitrogen-fixing ability by the ARA method. According to the above-described analysis, strain SG131T represents a novel species of the genus Propionivibrio, for which the name Propionivibrio soli sp. nov. is proposed. The type strain is SG131T (= GDMCC 1.3313T = JCM 35595T).

A novel strictly anaerobic sulfate-reducing diazotrophic bacterium Fundidesulfovibrio terrae sp. nov., isolated from paddy soil.

A strictly anaerobic sulfate-reducing strain, designated SG127T, was isolated from paddy soil. SG127T showed the highest 16S rRNA gene sequence similarity to the type strain of Fundidesulfovibrio magnetotacticus (98.2 %). A phylogenetic tree based on 16S rRNA gene sequences indicated that SG127T clustered with members of the genus Fundidesulfovibrio. Growth of SG127T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-9.0 (optimum, 7.0-8.0) and with 0-0.2 % (w/v) NaCl (optimally without NaCl). SG127T contained MK-7 as the only menaquinone and anteiso-C15 : 0, anteiso-C17 : 1ω9c, C18 : 0, iso-C14 : 0, iso-C15 : 0, iso-C16:0, iso-C16 : 1H, iso-C18 : 1H and summed feature nine as the major fatty acids. The genomic DNA G+C content of SG127T was 64.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SG127T and the closely related Fundidesulfovibrio magnetotacticus were 78.5% and 23.2 %, respectively, which were lower than the cut-off values (ANI 95-96% and dDDH 70 %) for prokaryotic species delineation. SG127T had desulfoviridin, possessed nitrogen fixation genes (nifHDK) and actively fixed nitrogen according to the acetylene reduction assay. On the basis of these results, strain SG127T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio terrae sp. nov. is proposed. The type strain is SG127T (= GDMCC 1.3137T = JCM 35589T).

Lederbergia citrea sp. nov., isolated from citrus rhizosphere.

Three Gram-positive-staining strains FJAT-49754T, FJAT-49682 and FJAT-49731 were isolated from the citrus rhizosphere soil sample. These strains showed the highest 16S rRNA gene sequence similarity with the type strain of Lederbergia panacisoli (97.8-97.9 %). The 16S rRNA gene sequence similarities between strains FJAT-49754T, FJAT-49682, and FJAT-49731 were 99.9 %. The average nucleotide identity (ANI) values between strains FJAT-49754T, FJAT-49682 and FJAT-49731 were above 96 %, while the ANI values with the members of the genus Lederbergia were below 95 %, which were below the cut-off level for prokaryotic species delineation. The above results suggest that strains FJAT-49754T, FJAT-49682 and FJAT-49731 belong to a novel species of the genus Lederbergia. Growth of strain FJAT-49754T was observed at 10-40 °C (optimum at 30 °C, pH 6.0-10.0 (optimum at pH 8.0), and NaCl tolerance up to 7 % (w/v) (optimum at 1 %). MK-7 was the only menaquinone detected in strain FJAT-49754T, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids of strain FJAT-49754T were anteiso-C15 : 0, iso-C15 : 0, and C16 : 0. The genomic DNA G+C content of strain FJAT-49754T was 38.7 %. Based on the above results, strain FJAT-49754T represents a novel species of the genus Lederbergia, for which the name Lederbergia citrea sp. nov., is proposed. The type strain is FJAT-49754T (=CCTCC AB 2019211T=LMG 31589T).

Geothrix fuzhouensis sp. nov. and Geothrix paludis sp. nov., two novel Fe(III)-reducing bacteria isolated from paddy soil.

Two anaerobic, Fe(III)-reducing and Gram-stain-negative strains, designated SG12T and SG195T, were isolated from paddy soils in Fujian Province, PR China. Phylogenetic trees based on 16S rRNA genes and conserved core genes from genomes indicated that strains SG12T and SG195T clustered with members of the genus Geothrix. The two strains showed the highest 16S rRNA sequences similarities to the type strains of 'Geothrix terrae' SG184T (98.4-99.6 %), 'Geothrix alkalitolerans' SG263T (98.4-99.6 %) and Geothrix fermentans DSM 14018T (98.2-98.8 %). The average nucleotide identity and digital DNA-DNA hybridization values between the two strains and the closely related Geothrix species were 85.1-93.5 % and 29.8-52.9 %, respectively, lower than the cut-off level for prokaryotic species delineation. The menaquinone was MK-8 in both strains. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. Additionally, the two strains possessed iron reduction ability and could utilize organics such as benzene and benzoic acid as electron donors to reduce ferric citrate to ferrous iron. Based on the morphological, biochemical, chemotaxonomic and genome data, the two isolated strains represent two novel species of the genus Geothrix, for which the names Geothrix fuzhouensis sp. nov. and Geothrix paludis sp. nov. are proposed. The type strains are SG12T (=GDMCC 1.3407T=JCM 39330T) and SG195T (= GDMCC 1.3308T=JCM 39327T), respectively.

Two novel alkalitolerant species Pseudalkalibacillus spartinae sp. nov. and Pseudalkalibacillus sedimenti sp. nov.

In this study, two novel alkalitolerant strains (FJAT-53046T and FJAT-53715T) were isolated from sediment samples collected in Zhangzhou, PR China. Phylogeny based on 16S rRNA gene sequences suggested that strains FJAT-53046T and FJAT-53715T were new members of the genus Pseudalkalibacillus. The two novel strains showed the highest 16S rRNA gene sequence similarity to Pseudalkalibacillus hwajinpoensis DSM 16206T, with values of 97.4 and 97.6 %, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains and the reference strain were 77.2 and 79.6 %, 20.9 and 30.2 %, respectively, which were below the prokaryotic species delineation thresholds. The ANI and dDDH values between strains FJAT-53046T and FJAT-53715T were 86.0 and 30.2 %, respectively, suggesting that they belonged to different species in the genus Pseudalkalibacillus. The major respiratory quinone in both strains was MK-7 and the major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids in both novel strains. Combined with results stemming from the determination of physical and biochemical characteristics, chemical properties, and genome analysis, strains FJAT-53046T and FJAT-53715T are proposed to represent two novel species of the genus Pseudalkalibacillus, for which the names Pseudalkalibacillus spartinae sp. nov. and Pseudalkalibacillus sedimenti sp. nov. are proposed. The type strains are FJAT-53046T (=GDMCC 1.3077T=JCM 35611T) and FJAT-53715T (=GDMCC 1.3076T=JCM 35610T), respectively.

Isolation and genomics of ten novel Shewanella species from mangrove wetland.

Mangrove bacteria largely compose the microbial community of the coastal ecosystem and are directly associated with nutrient cycling. In the present study, 12 Gram-negative and motile strains were isolated from a mangrove wetland in Zhangzhou, China. Pairwise comparisons (based on 16S rRNA gene sequences) and phylogenetic analysis indicated that these 12 strains belong to the genus Shewanella. The 16S rRNA gene sequence similarities among the 12 Shewanella strains and their related type strains ranged from 98.8 to 99.8 %, but they still could not be considered as known species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the 12 strains and their related type strains were below the cut-off values (ANI 95-96% and dDDH 70 %) for prokaryotic species delineation. The DNA G+C contents of the present study strains ranged from 44.4 to 53.8 %. The predominant menaquinone present in all strains was MK-7. The present study strains (except FJAT-53532T) also contained ubiquinones (Q-8 and Q-7). The polar lipid phosphatidylglycerol and fatty acid iso-C15 : 0 was noticed in all strains. Based on phenotypic, chemotaxonomic, phylogenetic and genomic comparisons, we propose that these 12 strains represent 10 novel species within the genus Shewanella, with the names Shewanella psychrotolerans sp. nov. (FJAT-53749T=GDMCC 1.2398T=KCTC 82649T), Shewanella zhangzhouensis sp. nov. (FJAT-52072T=MCCC 1K05363T=KCTC 82447T), Shewanella rhizosphaerae sp. nov. (FJAT-53764T=GDMCC 1.2349T=KCTC 82648T), Shewanella mesophila sp. nov. (FJAT-53870T=GDMCC 1.2346T= KCTC 82640T), Shewanella halotolerans sp. nov. (FJAT-53555T=GDMCC 1.2344T=KCTC 82645T), Shewanella aegiceratis sp. nov. (FJAT-53532T=GDMCC 1.2343T=KCTC 82644T), Shewanella alkalitolerans sp. nov. (FJAT-54031T=GDMCC 1.2347T=KCTC 82642T), Shewanella spartinae sp. nov. (FJAT-53681T=GDMCC 1.2345T=KCTC 82641T), Shewanella acanthi sp. nov. (FJAT-51860T=GDMCC 1.2342T=KCTC 82650T) and Shewanella mangrovisoli sp. nov. (FJAT-51754T=GDMCC 1.2341T= KCTC 82647T).

Cytobacillus citreus sp. nov., isolated from citrus rhizosphere soil.

A Gram-stain-positive, rod-shaped and motile strain, designated FJAT-49705T, was isolated from the citrus rhizosphere soil sample. Strain FJAT-49705T grew at 20-40 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, pH 7.0) with 0-5 % (w/v) NaCl (optimum, 2 %). Strain FJAT-49705T showed high 16S rRNA gene sequence similarity to 'Bacillus dafuensis' FJAT-25496T (99.7 %) and Cytobacillus solani FJAT-18043T (98.0 %). In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic trees (based on 71 bacterial single-copy genes), strain FJAT-49705T clustered with the members of the genus Cytobacillus. MK-7 was the only isoprenoid quinone present. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 36.9 %. The average nucleotide identity (ANI) values between FJAT-49705T and 'B. dafuensis' FJAT-25496T and C. solani FJAT-18043T were below the cut-off level (95-96 %) recommended as the ANI criterion for interspecies identity. Based on the above results, strain FJAT-49705T represents a novel species of the genus Cytobacillus, for which the name Cytobacillus citreus sp. nov. is proposed. The type strain is FJAT-49705T (=CCTCC AB 2019243T= LMG 31580T).

Prophage Induction Causes Geobacter Electroactive Biofilm Decay.

Sustaining a metabolically active electroactive biofilm (EAB) is essential for the high efficiency and durable operation of microbial fuel cells (MFCs). However, EABs usually decay during long-term operation, and, until now, the causes remain unknown. Here, we report that lysogenic phages can cause EAB decay in Geobacter sulfurreducens fuel cells. A cross-streak agar assay and bioinformatic analysis revealed the presence of prophages on the G. sulfurreducens genome, and a mitomycin C induction assay revealed the lysogenic to lytic transition of those prophages, resulting in a progressive decay in both current generation and the EAB. Furthermore, the addition of phages purified from decayed EAB resulted in accelerated decay of the EAB, thereafter contributing to a faster decline in current generation; otherwise, deleting prophage-related genes rescued the decay process. Our study provides the first evidence of an interaction between phages and electroactive bacteria and suggests that attack by phages is a primary cause of EAB decay, having significant implications in bioelectrochemical systems.