Zhi-Ping Zhong

Successful bioremediation of an aged and heavily contaminated soil using a microbial/plant combination strategy.

Bioremediation of an aged and heavily contaminated soil was performed using microbial remediation, phytoremediation, and microbial/phytoremediation. The removal efficiency of polycyclic aromatic hydrocarbons (PAHs) was in the order microbial/phytoremediation>microbial remediation≈phytoremediation>control. The removal percentage of microbial/phytoremediation (69.6%) was twice that of control. Kocuria sp. P10 significantly enhanced PAH removal (P<0.05) and ryegrass growth (P<0.01). Dehydrogenase activity increased steadily and was negatively correlated with total PAH content. Successional changes in soil microbial communities were also detected by pyrosequencing. The results indicated that biodiversity of the soil bacterial community gradually increased with time and was slightly lower in control, as indicated by operational taxonomic unit (OTU) numbers and Shannon-Wiener indices. Proportions of Betaproteobacteria and Gammaproteobacteria were consistently high in all groups. Actinobacteridae were initially predominant (>37.8%) but rapidly decreased to <4%. The proportions of Acidobacteria increased greatly and this increase was positively correlated with PAH removal. These findings indicate a healthy ecological progression and a role of Acidobacteria as an indicator of the process. This study provides new insights into the dynamics of community structure during bioremediation process and a possible basis for ecological assessment for bioremediation on a large scale.

Pilot scale ex-situ bioremediation of heavily PAHs-contaminated soil by indigenous microorganisms and bioaugmentation by a PAHs-degrading and bioemulsifier-producing strain.

This study aims at the remediation of heavily PAH-contaminated soil containing 375 mg of total PAHs per kilogram dry soil. Pilot scale bioremediation experiments were carried out by three approaches with contaminated soil from abandoned sites of Beijing Coking Plant using outdoor pot trials. The first approach was bioaugmentation with a bacterial strain which degrades PAH and produces bioemulsifier, the second approach comprised of biostimulation of indigenous microorganisms with supplementing nutrients and the last approach involved the combination of both biostimulation and bioaugmentation. An on-site land farming group was set as a control in which the total PAHs and 4-6 ring-PAHs were reduced by 23.4% and 10.1%, respectively after 175 days. Meanwhile, in the first approach group, the total PAHs and 4-6 ring-PAHs were reduced by 26.82% and 35.36%, respectively; in the second approach group both percentages were 33.9% and 11.0%, respectively; while in the third approach group, these pollutants were reduced by 43.9% and 55.0%, respectively. The results obtained suggested that biostimulation and bioaugmentation combined could significantly enhance the removal of PAHs in the contaminated soil.

Roseibium aquae sp. nov., isolated from a saline lake.

A Gram-staining-negative bacterium, strain DSG-S4-2(T), was isolated from Dasugan Lake, a saline lake (salinity 3.1%, w/v) in Qaidam basin, Qinghai, China and its taxonomic position was determined by using a polyphasic approach. Cells of strain DSG-S4-2(T) were non-spore-forming rods, 0.5-0.8 µm wide and 1.2-3.8 µm long and motile by means of a single polar flagellum. Strain DSG-S4-2(T) was strictly heterotrophic and aerobic, catalase-positive and oxidase-negative. PufLM and coxL genes were present, bacteriochlorophyll a (BChl a) and a carotenoid pigment were produced. Growth was observed in the presence of 0-8.0% (w/v) NaCl (optimum, 1.0-2.0%), at 20-40 °C (optimum, 35 °C) and pH 6.5-10.5 (optimum, pH 7.5-8.0). Strain DSG-S4-2(T) contained Q-10 as the sole respiratory quinone. The polar lipids contained two aminolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sulphoquinovosyldiacylglyceride, phosphatidylcholine and some unknown phospholipids, like the other members of the genus Roseibium. The predominant fatty acid (>70%) was summed feature 8 (C(18 : 1)ω7c and/or C(18 : 1)ω6c). The DNA G+C content was 61.4 mol% (determined from melting temperature). Phylogenetic trees (neighbour-joining, maximum-likelihood and maximum-parsimony) based on 16S rRNA gene sequences showed that strain DSG-S4-2(T) was associated with the members of the genus Roseibium, with highest 16S rRNA gene sequence similarity to Roseibium denhamense OCh 254(T) (96.3%) and Roseibium hamelinense OCh 368(T) (96.3%). Based on the data presented above, it is concluded that strain DSG-S4-2(T) represents a novel species of the genus Roseibium, for which the name Roseibium aquae sp. nov. is proposed. The type strain is DSG-S4-2(T) ( = CGMCC 1.12426(T) = JCM 19310(T)).

Prokaryotic community structure driven by salinity and ionic concentrations in plateau lakes of the Tibetan plateau

ABSTRACT The prokaryotic community composition and diversity and the distribution patterns at various taxonomic levels across gradients of salinity and physiochemical properties in the surface waters of seven plateau lakes in the Qaidam Basin, Tibetan Plateau, were evaluated using Illumina MiSeq sequencing. These lakes included Lakes Keluke (salinity, <1 g/liter), Qing (salinity, 5.5 to 6.6 g/liter), Tuosu (salinity, 24 to 35 g/liter), Dasugan (salinity, 30 to 33 g/liter), Gahai (salinity, 92 to 96 g/liter), Xiaochaidan (salinity, 94 to 99 g/liter), and Gasikule (salinity, 317 to 344 g/liter). The communities were dominated by Bacteria in lakes with salinities of <100 g/liter and by Archaea in Lake Gasikule. The clades At12OctB3 and Salinibacter, previously reported only in hypersaline environments, were found in a hyposaline lake (salinity, 5.5 to 6.6 g/liter) at an abundance of ∼1.0%, indicating their ecological plasticity. Salinity and the concentrations of the chemical ions whose concentrations covary with salinity (Mg2+, K+, Cl−, Na+, SO4 2−, and Ca2+) were found to be the primary environmental factors that directly or indirectly determined the composition and diversity at the level of individual clades as well as entire prokaryotic communities. The distribution patterns of two phyla, five classes, five orders, five families, and three genera were well predicted by salinity. The variation of the prokaryotic community structure also significantly correlated with the dissolved oxygen concentration, pH, the total nitrogen concentration, and the PO4 3− concentration. Such correlations varied depending on the taxonomic level, demonstrating the importance of comprehensive correlation analyses at various taxonomic levels in evaluating the effects of environmental variable factors on prokaryotic community structures. Our findings clarify the distribution patterns of the prokaryotic community composition in plateau lakes at the levels of individual clades as well as whole communities along gradients of salinity and ionic concentrations.

Pseudomonas salina sp. nov., isolated from a salt lake.

A Gram-staining-negative, facultatively aerobic bacterium, strain XCD-X85(T), was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9%, w/v) in Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X85(T) were non-endospore-forming rods, 0.4-0.6 μm wide and 1.0-1.6 μm long, and motile by means of a single polar flagellum. Strain XCD-X85(T) was catalase- and oxidase-positive. Growth was observed in the presence of 0-12.0% (w/v) NaCl (optimum, 1.0-2.0%) and at 4-35 °C (optimum, 25-30 °C) and pH 6.5-10.5 (optimum, pH 8.0-8.5). Strain XCD-X85(T) contained (>10%) summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C12 : 0, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the predominant fatty acids. The major respiratory quinone was ubiquinone 9 (Q-9). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 57.4 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X85(T) was associated with the genus Pseudomonas, and showed highest 16S rRNA gene sequence similarities to Pseudomonas pelagia CL-AP6(T) (99.0%) and Pseudomonas bauzanensis BZ93(T) (96.8%). DNA-DNA relatedness of strain XCD-X85T to P. pelagia JCM 15562(T) was 19 ± 1%. On the basis of the data presented above, it is concluded that strain XCD-X85(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas salina sp. nov. is proposed. The type strain is XCD-X85(T) ( = CGMCC 1.12482(T) = JCM 19469(T)).

Planktosalinus lacus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a salt lake.

A Gram-staining-negative bacterium, strain X14M-14T, was isolated from a salt lake (Lake Xiaochaidan) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain X14M-14T were non-spore-forming, non-motile rods. Strain X14M-14T was strictly heterotrophic and aerobic, catalase-positive and oxidase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain X14M-14T belonged to the family Flavobacteriaceae and formed a distinct lineage that was independent of the most closely related genera: Aequorivita (16S rRNA gene sequence similarities, 91.8-93.1 %) and Salinimicrobium (91.5-92.4 %). Strain X14M-14T contained MK-6 as the major respiratory quinone, and phosphatidylethanolamine and two unknown lipids as the major polar lipids. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The presence of iso-C15 : 1 G as a predominant fatty acid could distinguish this strain clearly from the most closely related genera in the family Flavobacteriaceae. The DNA G+C content was 36.6 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain X14M-14T represents a novel genus and species of the family Flavobacteriaceae, for which the name Planktosalinus lacus gen. nov., sp. nov. is proposed. The type strain is X14M-14T ( = CGMCC 1.12924T = KCTC 42675T).

Thalassotalea marina sp. nov., isolated from a marine recirculating aquaculture system, reclassification of Thalassomonas eurytherma as Thalassotalea eurytherma comb. nov. and emended description of the genus Thalassotalea.

A Gram-stain-negative, facultatively anaerobic bacterium, strain QBLM2T, was isolated from rearing water of a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated through a polyphasic approach. Cells of strain QBLM2T were non-spore-forming rods, motile by means of a single polar flagellum. Positive for oxidase and catalase. Growth occurred at 15-40 °C (optimum 30 °C), at pH 6.5-10.5 (optimum pH 7.5-8.5) and in the presence of 0-5.0 % (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QBLM2T formed a distinct lineage within the genus Thalassotalea and exhibited sequence similarities of 94.5-96.3 % to members of the genus Thalassotalea. The predominant fatty acids (>10 %) were C17 : 1ω8c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 (Q-8) was the major ubiquinone. The DNA G+C content was 37.1 mol%. Based on the data above, strain QBLM2T is considered to represent a novel species of the genus Thalassotalea, for which the name Thalassotalea marina sp. nov. is proposed. The type strain is QBLM2T ( = CGMCC 1.12814T = KCTC 42731T). Phylogenetic analyses indicated that Thalassomonas eurytherma Za6a-12T fell within the genus Thalassotalea, so it is reclassified as Thalassotalea eurytherma comb. nov. and the description of the genus Thalassotalea is emended.

Rheinheimera tuosuensis sp. nov., isolated from a saline lake.

A Gram-staining-negative bacterium, strain TS-T4(T), was isolated from Tuosu Lake, a saline lake (salinity 5.4 %, w/w) in Qaidam basin, Qinghai, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain TS-T4(T) were non-spore-forming rods, 0.4-0.8 µm wide and 1.7-2.3 µm long, and motile by means of a single polar flagellum. Strain TS-T4(T) was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Growth was observed in the presence of 0-7.0 % (w/v) NaCl (optimum, 3.0-4.0 %) and at 4-40 °C (optimum, 30-35 °C) and pH 7.0-10.5 (optimum, pH 8.5-9.0). Strain TS-T4(T) contained Q-8 as the sole respiratory quinone and phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids, as for other members of the genus Rheinheimera. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C17 : 1ω8c and C18 : 1ω7c. The DNA G+C content was 50.2 mol% (Tm). Phylogenetic trees based on sequences of the 16S rRNA gene and a conserved portion of the gyrase B gene (gyrB) showed that strain TS-T4(T) was associated with the genus Rheinheimera; the strain showed the highest 16S rRNA gene sequence similarity to Rheinheimera longhuensis LH2-2(T) (97.1 %) and then to Rheinheimera pacifica KMM 1406(T) (97.0 %). DNA-DNA relatedness of strain TS-T4(T) with R. longhuensis LH2-2(T) and R. pacifica NBRC 103167 was 53±2.5 and 48±2 %, respectively. Based on the data presented, it is concluded that TS-T4(T) represents a novel species of the genus Rheinheimera, for which the name Rheinheimera tuosuensis sp. nov. is proposed. The type strain is TS-T4(T) ( = CGMCC 1.12461(T) = JCM 19264(T)).

Marinobacter halophilus sp. nov., a halophilic bacterium isolated from a salt lake

A Gram-staining-negative bacterium, strain XCD-X12(T), was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9%, w/w) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X12(T) were non-spore-forming rods, 0.4-0.7 μm wide, 2.1-3.2 μm long and motile with a single polar flagellum. Strain XCD-X12(T) was strictly aerobic and catalase- and oxidase-positive. Growth was observed in the presence of 0-20.0% (w/v) NaCl (optimum, 4.0-8.0%), at 4-35 °C (optimum, 30 °C) and at pH 6.5-10.5 (optimum, pH 8.5). It contained Q-9 as the predominant respiratory quinone. The major fatty acids (>10.0%) were C16 : 0, C16 : 1ω9c and C18 : 1ω9c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and an uncharacterized aminophospholipid. The DNA G+C content was 55.6 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X12(T) was associated with the genus Marinobacter, and showed the highest 16S rRNA gene sequence similarity to Marinobacter hydrocarbonoclasticus ATCC 49840(T) (97.4%), M. vinifirmus FB1(T) (96.8%), M. excellens KMM 3809(T) (96.8%) and M. antarcticus ZS2-30(T) (96.7%). DNA-DNA relatedness of strain XCD-X12(T) to M. hydrocarbonoclasticus CGMCC 1.7683(T) was 34 ± 5%. Based on these data, it is concluded that strain XCD-X12(T) represents a novel species of the genus Marinobacter, for which the name Marinobacter halophilus sp. nov. is proposed. The type strain is XCD-X12(T) ( = CGMCC 1.12481(T)= JCM 30472(T)).

Cribrihabitans marinus gen. nov., sp nov., isolated from a biological filter in a marine recirculating aquaculture system

A Gram-negative bacterium, strain CZ-AM5(T), was isolated from an aerated biological filter in a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated by using a polyphasic approach. Cells of strain CZ-AM5(T) were non-spore-forming rods, 0.5-0.8 µm wide and 1.2-2.0 µm long, and motile by means of one or two polar or lateral flagella. Strain CZ-AM5(T) was strictly aerobic, heterotrophic, oxidase-negative and catalase-positive. Growth occurred at 15-40 °C (optimum, 30-35 °C), at pH 6.5-10.5 (optimum, pH 7.0-7.5) and in the presence of 0-12.0 % (w/v) NaCl (optimum, 4.0 %). The predominant fatty acid was C18 : 1ω7c (80.3 %). Ubiquinone 10 (Q-10) was the sole respiratory quinone. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown aminolipid, an unknown phospholipid and three unknown lipids. The DNA G+C content was 60.4 mol%. Strain CZ-AM5(T) showed the highest 16S rRNA gene sequence similarity (96.5 %) to Phaeobacter caeruleus LMG 24369(T); it exhibited 16S rRNA gene sequence similarity of 95.0-96.5, 95.2-96.3, 96.2, 94.6-95.7 and 94.8-95.8 % to members of the genera Phaeobacter, Ruegeria, Citreimonas, Leisingera and Donghicola, respectively. However, phylogenetic trees based on 16S rRNA gene sequences showed that strain CZ-AM5(T) did not join any of the above genera, but formed a distinct lineage in the trees. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain CZ-AM5(T) is considered to represent a novel genus and species of the family Rhodobacteraceae, for which the name Cribrihabitans marinus gen. nov., sp. nov. is proposed. The type strain of Cribrihabitans marinus is CZ-AM5(T) ( = CGMCC 1.13219(T) = JCM 19401(T)).