Relationships between two Pseudoalteromonas strains isolated from the Canada Basin and the Southern Ocean using a polyphasic approach

The evolutionary relationships and taxonomic position of two marine planktonic bacterial strains BSw20211 and BSw10014, isolated from the Canada Basin and from the Southern Ocean, respectively, were determined using a polyphasic taxonomic approach. There was a close phylogenetic relationship between the two strains and most phenotypic properties were shared. Nonetheless, they were found to belong to different species of the genus Pseudoalteromonas on the basis of genotypic analyses. Findings were consistent with the suggestion that gyrB gene sequence comparison and DNA-DNA relatedness might better define phylogenetic relationships of bacteria at the species level. However, a cut-off value of 90% gyrB gene sequence similarity was not reliable for the differentiation of species within the genus Pseudoalteromonas

PAHs contamination and PAH-degrading bacteria inXiamen Western Sea

Six stations were established in Xiamen Western Sea (24°29’ N, 118°04’ E) on summer and autumn cruises in July and October 2001 to investigate the level of polyaromatic hydrocarbons (PAHs) and PAHs-degrading bacteria in surface water and sediments. PAHs in the surface water were mainly dominated by low molecular weight PAH compounds (2–3 rings PAH) in July and by high molecular weight PAH compounds (4–6 rings PAH)in October. PAHs in sediments were mainly dominated by high molecular weight PAH compounds (4–6). The percentage of 4–6 rings PAH to total PAHs ranged from 80.4 to 94.9% in July and 78.3 to 88.7% in October. No correlation was found between Fluoranthene-degrading bacteria numbers and Fluoranthene concentration among different stations in the surface water on the two cruises, and the same situation occurred between Pyrene-degrading bacteria numbers and pyrene concentration. But the numbers of fluorene- and phenanthrenedegrading bacteria were positively related to the fluorene and phenanthrene concentrations respectively. In the sediments, a significant positive relationship was found between PAH-degrading bacteria and PAHs concentration, except at station 6 on the two cruises

Soil bacterial diversity is associated with human population density in urban greenspaces

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of American Chemical Society for personal use, not for redistribution. The definitive version was published in Environmental Science and Technology 52 (2018): 5115–5124, doi:10.1021/acs.est.7b06417.Urban greenspaces provide extensive ecosystem services, including pollutant remediation, water management, carbon maintenance, and nutrient cycling. However, while the urban soil microbiota underpin these services, we still have limited understanding of the factors that influence their distribution. We characterized soil bacterial communities from turf-grasses associated with urban parks, streets and residential sites across a major urban environment, including a gradient of human population density. Bacterial diversity was significantly positively correlated with the population density; and species diversity was greater in park and street soils, compared to residential soils. Population density and greenspace type also led to significant differences in the microbial community composition that was also significantly correlated with soil pH, moisture and texture. Co-occurrence network analysis revealed that microbial guilds in urban soils were well correlated. Abundant soil microbes in high density population areas had fewer interactions, while abundant bacteria in high moisture soils had more interactions. These results indicate the significant influence of changes in urban demographics and land-use on soil microbial communities. As urbanization is rapidly growing across the planet, it is important to improve our understanding of the consequences of urban zoning on the soil microbiota.This study is supported by the Earth Microbiome Project (http://www.earthmicrobiome.org/) and the China Scholarship Council (http://en.csc.edu.cn/).2019-04-0

Preliminary study on PAH degradation by bacteria from contaminated sediments in Xiamen Western Sea, Fujian, China

In order to estimate the biodegradation of three polycyclic aromatic hydrocarbons (PAHs) compounds, bacterial strains were isolated from marine sediments in three heavily contaminated sites (Yuandang Lake, Dongdu Port and Aquacultural zones in Maluan Bay) in Xiamen Western Sea. The results show three bacterial strains, which used pyrene as the sole carbon source, were identified as strains of Aureobacterium sp., Arthrobacter sp., Rhodococcus sp. The PAH-degrading bacteria isolated had a strong ability to degrade phenanhrene,fluoranthene and pyrene at different degradation rates. The highest degradation rate was observed when three PAH compounds were mixed with an individual strain in the medium. The three PAHs were degraded after one week with a degradation rate of 89.94% for phenanthrene and 93.4 % for both of fluoranthene and pyrene.In addition, after 25 days of incubation, the degradation rate was 99.98 % for phenanthrene and 99.97 % for both of fluoranthene and pyrene. Optical density was measured to estimate bacterial growth during the degradation of PAHs. Highest levels of bacterial growth were observed with a three PAH mixture in the culture, suggesting that the concentration of PAHs influenced bacterial growth and the highest levels of degradation for most series were detected after one week of incubation.Supported by the NSFC (No.30070157, 40206015), and the Scientific Fund of Quanzhou City (No. Z200234)

Occurrence and quantification of fungi and detection of mycotoxigenic fungi in drinking water in Xiamen City, China

National High-Tech R&D Program of China (863 Program) [2012AA062607]; National Natural Scientific Foundation of China [51278482, 51078343]; 100 Talents Program of Chinese Academy of SciencesFungi are known to play an important role in nutrient and carbon cycling, and the occurrence of fungi in the water supply may result in a variety of human health problems. This study aimed to investigate the occurrence and frequency of various fungi in drinking water over a one-year period. The study also aimed to quantify the fungal presence using real-time PCR, and to effectively detect mycotoxigenic fungi in a variety of water sources. Water samples were collected from different water systems (surface water, public system water, house water, and tank water), from different sites (n=15) in Xiamen, China. Each month from February 2011 to January 2012, 22 water samples were collected and analyzed. The results showed that surface water samples possessed a higher frequency of fungi than did the other water samples. Identification of fungal species was conducted using morphological and molecular methods. The most dominant fungi found were Aspergillus spp., Fusarium spp., Pencillium spp., Trichoderma spp., Mucor sp., and Rhizopus sp. Notably, the more-frequency observed fungi in the tap water of houses and public systems were Fusarium sp., Exophiala sp., and Phialophora sp. Meanwhile, mycotoxigenic fungi were detected in some water samples at different times. The strains isolated from samples collected in September to November had the aflatoxigenic fungi, and for fumonisin and trichothecenes, the fungi strains were re-isolated from water in November and December. (C) 2012 Elsevier B.V. All rights reserved

A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom.

Phytoplankton blooms are a worldwide problem and can greatly affect ecological processes in aquatic systems, but its impacts on the functional potential of microbial communities are limited. In this study, a high-throughput microarray-based technology (GeoChip) was used to profile the functional potential of free-living microbes from the Xiamen Sea Area in response to a 2011 Akashiwo sanguinea bloom. The bloom altered the overall community functional structure. Genes that were significantly (p < 0.05) increased during the bloom included carbon degradation genes and genes involved in nitrogen (N) and/or phosphorus (P) limitation stress. Such significantly changed genes were well explained by chosen environmental factors (COD, nitrite-N, nitrate-N, dissolved inorganic phosphorus, chlorophyll-a and algal density). Overall results suggested that this bloom might enhance the microbial converting of nitrate to N2 and ammonia nitrogen, decrease P removal from seawater, activate the glyoxylate cycle, and reduce infection activity of bacteriophage. This study presents new information on the relationship of algae to other microbes in aquatic systems, and provides new insights into our understanding of ecological impacts of phytoplankton blooms

The distribution characteristics of bacterial β-glucosidase activity in Taiwan strait

Twenty stations were established in the near-shore regions of South Fujian Shoal (116°10’-119°00’E,21°20’-24°10’N) on summer and winter cruises during the period from August 1997 and February to March 1998. The distribution pattern of marine bacterial β-glucosidase activity (β-GlcA) has been investigated by using fluorogenic model substrate (FMS) technique in order to have better understanding of the β-GlcA, as well as its relation to marine bacterial biomass, productivity and environmental factors in Taiwan strait. The results showed that: (1) In summer, the average of β-GlcA at the Southern stations of Taiwan strait was 1.94 nmol/1 h. While in winter, the average of β-GlcA at the Northern stations was 0.86 nmol/1 h and the range of variation (0.34–1.89 nmol/1 h) was much more narrow than that in summer (0.31–8.1 nmol/1 h). (2) According to the carbon conversion factor, the β-GlcA was 0.14 and 0.062 ugc/1 h in summer and winter respectively. These β-GlcA values were higher than the bacterial production of the two seasons respectively. (3) The β-GlcA gradually rises from offshore water to near-shore water. (4) The correlation between the β-GlcA and the bacterial secondary production was not so obvious. (5) The correlation between the section distributions, daily varying of the β-GlcA and the bacterial production was not obvious. (6) In the surface water, the distribution character of free-state β-GlcA from bacteria was equal to that of the total β-GlcA in the whole sea area

PAH-biodegradation potential of indigenous microorganisms: evidence from the respiratory activity of surface sediments in the Quanzhou Bay in China

Seven stations were established in the Quanzhou Bay (24.73 degrees-24.96 degrees N, 118.50 degrees-118.70 degrees E) in China on three cruises to determine the concentrations of polycyclic aromatic hydrocarbons (PAHs) and the numbers of PAH-degrading bacteria in surface sediments. Assessing the biodegradation potential of indigenous microorganisms by measuring the respiratory intensity with the addition of PAHs in sediment samples was also one of the aims of this study. The results show that the total PAH concentrations of the sediments were 99.23-345.53 ng/g dry weight (d.w.), and the PAHs composition pattern in the sediments was dominated by phenanthrene, fluoranthene and pyrene. The numbers of phenanthrene. fluoranthene and pyrene-degrading bacteria during three cruises were 1.42 x 10(3)-8.93 x 10(4) CFU/g d.w., 8.29 x 10(3)-9.43 x 10(4) CFU/g d.w. and 7.05 x 10(3)-9.43 x(4) CFU/g d.w., respectively. The addition of three model PAH compounds (phenanthrene, fluoranthene and pyrene) showed a great influence on the increasing of the microbial activity in the sediments. And there was a significant correlation among the change of respiratory activity, PAH concentration and the number of PAH-degrading bacteria. The change in respiratory activity under PAHs selective pressure could, to a certain extent, indicate the potential degradative activity of the PAH-degrading microbial community.The National High Technology Research and Development Program ("863" Program) of China [2008AA09Z408]; National Natural Science Foundation of China [40576054]; Program for Changjiang Scholars and Innovative Research Team in University [40821063]; Science and Technology Foundation of Fujian Province, China [2008Y0061

LSU rDNA based RFLP assays for the routine identification of Gambierdiscus species

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Harmful Algae 66 (2017): 20-28, doi:10.1016/j.hal.2017.04.009.Gambierdiscus is a genus of benthic dinoflagellates commonly associated with ciguatera fish poisoning (CFP), which is generally found in tropical or sub-tropical regions around the world. Morphologically similar species within the genus can vary in toxicity; however, species identifications are difficult or sometimes impossible using light microscopy. DNA sequencing of ribosomal RNA genes (rDNA) is thus often used to identify and describe Gambierdiscus species and ribotypes, but the expense and time can be prohibitive for routine culture screening and/or large-scale monitoring programs. This study describes a restriction fragment length polymorphism (RFLP) typing method based on analysis of the large subunit ribosomal RNA gene (rDNA) that can successfully identify at least nine of the described Gambierdiscus species and two Fukuyoa species. The software programs DNAMAN 6.0 and Restriction Enzyme Picker were used to identify a set of restriction enzymes (SpeI, HpyCH4IV, and TaqαI) capable of distinguishing most of the known Gambierdiscus species for which DNA sequences were available. This assay was tested using in silico analysis and cultured isolates, and species identifications of isolates assigned by RFLP typing were confirmed by DNA sequencing. To verify the assay and assess intra-specific heterogeneity in RFLP patterns, identifications of 63 Gambierdiscus isolates comprising ten Gambierdiscus species, one ribotype, and two Fukuyoa species were confirmed using RFLP typing, and this method was subsequently employed in the routine identification of isolates collected from the Caribbean Sea. The RFLP assay presented here reduces the time and cost associated with morphological identification via scanning electron microscopy and/or DNA sequencing, and provides a phylogenetically sensitive method for routine Gambierdiscus species assignment.Funding for this study was provided by the U.S. National Oceanic and Atmospheric Administration ECOHAB program (CiguaHAB; Cooperative Agreement NA11NOS4780060, NA11NOS4780028), the China Scholarship Council and Natural Science Foundation of China (No. 41606137, 41606136), and the Guangxi Natural Science Foundation (2015GXNSFCA139003, 2016GXNSFBA380037)

Screening of PAH-degrading bacteria in a mangrove swamp using PCR-RFLP

There are abundant PAH-degrading bacteria in mangrove sediments, and it is very important to screen the high efficiency degraders in order to perform bioremediation of PAH polluted environments. In order to obtain the more highly efficient PAH-degrading bacteria from a mangrove swamp, we first obtained 62 strains of PAH-degrading bacteria using traditional culture methods and based on their morphological characteristics. We then used the modern molecular biological technology of PCR-RFLP, in which the 16S rDNA of these strains were digested by different enzymes. Based on differences in the PCR-RFLP profiles, we obtained five strains of phenanthrene-degrading bacteria, five strains of pyrene-degrading bacteria, four strains of fluoranthene-degrading bacteria, five strains of benzo[a]pyrene-degrading bacteria and two strains of mixed PAH-degrading bacteria (including phenanthrene, pyrene, fluoranthene and benzo[a]pyrene). Finally, a total of 14 different PAH-degrading bacteria were obtained. The 16S rDNA sequences of these strains were aligned with the BLAST program on the NCBI website and it was found that they belonged to the alpha-proteobacteria and gamma-proteobacteria, including four strains, where the similarities were no more than 97% and which were suspected therefore to be new species. This study indicated that PCR-RFLP was a very important method to screen degrading-bacteria, and also a significant molecular biological tool for the rapid classification and accurate identification of many different strains. On the other hand, it also showed that rich bacterial resources existed in mangrove areas, and that exploring and developing the functional microorganism from these mangrove areas would have wide use in the study of bioremediation of contaminated environments in the future. (C) 2010 Elsevier Ltd. All rights reserved.National Natural Science Foundation of China [40976069, 40930847, 30710103908, 30930017, 30940002]; National Programs for High Technology Research and Development of China [2008AA09Z408]; Fujian Province Universit