Alcanivorax indicus sp. nov., isolated from seawater

Alcanivorax quisquiliarum sp. nov., isolated from anaerobic fermentation liquid of food waste by high-throughput cultivation

Strain CY1518^T was isolated from an anaerobic fermentation liquid of food waste treatment plant in Beijing, PR China, and characterized to assess its taxonomy. Cells of CY1518^T were Gram-stain-negative, oxidase-negative, catalase-positive and ellipsoidal. Growth occurred at 20-42 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8) and with 0-6.0 % (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CY1518^T belongs to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax pacificus W11-5^T (95.97 %), followed by Alcanivorax indicus SW127^T (95.08%). The similarity between strain CY1518^T and other strains of Alcanivorax was less than 95 %. The genomic DNA G+C content of strain CY1518^T was 60.88 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CY1518^T and the closely related taxa A. pacificus W11-5^T and A. indicus SW127^T were 77.61, 78.03 and 21.2 % and 74.15, 70.02 and 19.3%, respectively. The strain was able to use d-serine, Tween 40 and some organic acid compounds for growth. The polar lipids comprised aminophospholipid, diphosphatidylglycerol, glycolipid, an unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. The principal fatty acids (>5 %) were C_19 : 0 cyclo ω8c (36.3%), C_16 : 0 (32.3%), C_12 : 0 3-OH (8.3%) and C_12 : 0 (7.6%). Based on its phenotypic, genotypic and genomic characteristics, strain CY1518^T represents a novel species in the genus Alcanivorax, for which the name Alcanivorax quisquiliarum sp. nov. is proposed. The type strain is CY1518^T (=GDMCC 1.2918^T=JCM 35120^T).

Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov

The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.

Petroleum spill bioremediation by an indigenous constructed bacterial consortium in marine environments

In the process of marine oil spill remediation, adding highly efficient oil degrading microorganisms can effectively promote oil degradation. However, in practice, the effect is far less than expected due to the inadaptability of microorganisms to the environment and their disadvantage in the competition with indigenous bacteria for nutrients. In this article, four strains of oil degrading bacteria were isolated from seawater in Jiaozhou Bay, China, where a crude oil pipeline explosion occurred seven years ago. Results of high-throughput sequencing, diesel degradation tests and surface activity tests indicated that Peseudomonas aeruginosa ZS1 was a highly efficient petroleum degrading bacterium with the ability to produce surface active substances. A diesel oil-degrading bacterial consortium (named SA) was constructed by ZS1 and another oil degrading bacteria by diesel degradation test. Degradation products analysis indicated that SA has a good ability to degrade short chain alkanes, especially n-alkanes (C₁₀-C₁₈). Community structure analysis showed that OTUs of Alcanivorax, Peseudomona, Ruegeria, Pseudophaeobacter, Hyphomonas and Thalassospira on genus level increased after the oil spill and remained stable throughout the recovery period. Most of these enriched microorganisms were related to known alkane and hydrocarbon degraders by the previous study. However, it is the first time to report that Pseudophaeobacter was enriched by using diesel as the sole carbon source. The results also indicated that ZS1 may have a dominant position in competition with indigenous bacteria. Oil pollution has an obvious selective effect on marine microorganisms. Although the oil degradation was promoted after SA injection, the recovery of microbial community structure took a longer time.

Effects of Turning Frequency on Ammonia Emission during the Composting of Chicken Manure and Soybean Straw

Here, we investigated the impact of different turning frequency (TF) on dynamic changes of N fractions, NH3 emission and bacterial/archaeal community during chicken manure composting. Compared to higher TF (i.e., turning every 1 or 3 days in CMS1 or CMS3 treatments, respectively), lower TF (i.e., turning every 5 or 7 days in CMS5 or CMS7 treatments, respectively) decreased NH3 emission by 11.42-18.95%. Compared with CMS1, CMS3 and CMS7 treatments, the total nitrogen loss of CMS5 decreased by 38.03%, 17.06% and 24.76%, respectively. Ammonia oxidizing bacterial/archaeal (AOB/AOA) communities analysis revealed that the relative abundance of Nitrosospira and Nitrososphaera was higher in lower TF treatment during the thermophilic and cooling stages, which could contribute to the reduction of NH3 emission. Thus, different TF had a great influence on NH3 emission and microbial community during composting. It is practically feasible to increase the abundance of AOB/AOA through adjusting TF and reduce NH3 emission the loss of nitrogen during chicken manure composting.

Alcanivorax limicola sp. nov., isolated from a soda alkali-saline soil

An alkaliphilic and aerobic bacterium, designated as strain JB21^T, was isolated from a soda alkali-saline soil sample in Heilongjiang, Northeast China. Strain JB21^T is a Gram-stain-negative, rod-shaped, non-motile and amylase-positive bacterium. Growth occurred at 15-45 °C (optimum, 35-37 °C), in the presence of 0-15.0% (w/v) NaCl (optimum, 1.0%) and at pH 6.5-10.5 (optimum, pH 8.5-9.5). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JB21^T was most closely related to type strains of the genus Alcanivorax, with the highest sequence similarity to Alcanivorax indicus SW127^T (96.3%), and shared 95.4-93.1% sequence identity with other valid type strains of this genus. The major cellular fatty acids identified were C_16:0 and summed feature 8 (C_18:1ω6c and/or C_18:1ω7c). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The genomic G + C content of strain JB21^T was 61.3 mol%. The digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) between strain JB21^T and type strains of the genus Alcanivorax were 18.3-23.2% and 69.2-79.0%, respectively. On the basis of its phenotypic and phylogenetic characteristics, we suggest the creation of a new species within the Alcanivorax genus, named Alcanivorax limicola sp. nov., type strain JB21^T (= CGMCC 1.16632^T = JCM 33717^T).

Alcanivorax profundimaris sp. nov., a Novel Marine Hydrocarbonoclastic Bacterium Isolated from Seawater and Deep-Sea Sediment

Two novel Alcanivorax-related strains, designated ST75FaO-1^T and 521-1, were isolated from the seawater of the South China Sea and the deep-sea sediment of the West Pacific Ocean, respectively. Both strains are Gram-stain-negative, rod-shaped, and non-motile, and grow at 10-40 °C, pH 5.0-10.0, in the presence of 1.0-15.0% (w/v) NaCl. Their 16S rRNA gene sequences showed 99.9% similarity. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that both strains belong to the genus Alcanivorax, and share 92.9-98.1% sequence similarity with all valid type strains of this genus, with the highest similarity being to type strain Alcanivorax venustensis DSM 13974^T (98.0-98.1%). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity values between strains ST75FaO-1^T and 521-1 were 75.7% and 97.1%, respectively, while the corresponding values with A. venustensis DSM 13974^T were only 25.4-25.6% and 82.4-82.7%, respectively. The two strains contained similar major cellular fatty acids including C_16:0, C_18:1 ω7c/ω6c, C_19:0 cyclo ω8c, C_16:1 ω7c/ω6c, C_12:0 3-OH, and C_12:0. The genomic G + C content of strains ST75FaO-1^T and 521-1 were 66.3% and 66.1%, respectively. Phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, and one unidentified polar lipid were present in both strains. On the basis of phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Alcanivorax, for which the name Alcanivorax profundimaris sp. nov. is proposed. The type strain is ST75FaO-1^T (= MCCC 1A17714^T = KCTC 82142^T).

Alcanivorax sediminis sp. nov., isolated from deep-sea sediment of the Pacific Ocean

A taxonomic study was carried out on strain PA15-N-34^T, which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0-15.0% NaCl and at temperatures of 10-45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34^T belonged to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax profundi MTEO17^T (97.7 %), followed by Alcanivorax nanhaiticus 19 m-6^T (97.3 %) and 12 other species of the genus Alcanivorax (93.4 %-97.0 %). The average nucleotide identity and DNA-DNA hybridization values between strain PA15-N-34^T and type strains of the genus Alcanivorax were 71.46-81.78% and 18.7-25.2 %, respectively. The principal fatty acids (>10 %) were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c; 31.2 %), C_16 : 0 (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34^T represents a novel species within the genus Alcanivorax, for which the name Alcanivorax sediminis sp. nov. is proposed, with the type strain PA15-N-34^T (=MCCC 1A14738^T=KCTC 72163^T).