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      Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China

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          Abstract

          The bacterioplankton community composition’s (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao’an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria.

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          A trophic state index for lakes1

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            Using ecological diversity measures with bacterial communities.

            Abstract There are many ecological diversity measures, but their suitability for use with highly diverse bacterial communities is unclear and seldom considered. We assessed a range of species richness and evenness/dominance indices, and the use of species abundance models using samples of bacteria from zinc-contaminated and control soils. Bacteria were assigned to operational taxonomic units (OTUs) using amplified ribosomal DNA restriction analysis of 236 clones from each soil. The reduced diversity apparent in the contaminated soil was reflected by the diversity indices to varying degrees. The number of clones analysed and the weighting given to rare vs. abundant OTUs are the most important considerations when selecting measures. Our preferences, arrived at using theory and practical experience, include: the log series index alpha; the Q statistic (but only if coverage is 50% or more); the Berger-Parker and Simpson's indices, although their ecological relevance may be limited; and, unexpectedly, the Shannon-Wiener and Shannon evenness indices, even though their meanings may not be clear and their values inaccurate when coverage is low. For extrapolation, the equation for the log series distribution seems the best for extrapolating from OTU accumulation curves while non-parametric methods, such as Chao 1, show promise for estimating total OTU richness. Due to a preponderance of single-occurrence OTUs, none of the five species abundance models fit the OTU abundance distribution of the control soil, but both the log and log normal models fit the less diverse contaminated soil. Species abundance models are useful, irrespective of coverage, because they address the whole distribution of a sample, aiding comparison by revealing overall trends as well as specific changes in particular abundance classes.
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              Current Perspectives on Viable but Non-Culturable (VBNC) Pathogenic Bacteria

              Under stress conditions, many species of bacteria enter into starvation mode of metabolism or a physiologically viable but non-culturable (VBNC) state. Several human pathogenic bacteria have been reported to enter into the VBNC state under these conditions. The pathogenic VBNC bacteria cannot be grown using conventional culture media, although they continue to retain their viability and express their virulence. Though there have been debates on the VBNC concept in the past, several molecular studies have shown that not only can the VBNC state be induced under in vitro conditions but also that resuscitation from this state is possible under appropriate conditions. The most notable advance in resuscitating VBNC bacteria is the discovery of resuscitation-promoting factor (Rpf), which is a bacterial cytokines found in both Gram-positive and Gram-negative organisms. VBNC state is a survival strategy adopted by the bacteria, which has important implication in several fields, including environmental monitoring, food technology, and infectious disease management; and hence it is important to investigate the association of bacterial pathogens under VBNC state and the water/foodborne outbreaks. In this review, we describe various aspects of VBNC bacteria, which include their proteomic and genetic profiles under the VBNC state, conditions of resuscitation, methods of detection, antibiotic resistance, and observations on Rpf.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Int J Environ Res Public Health
                Int J Environ Res Public Health
                ijerph
                International Journal of Environmental Research and Public Health
                MDPI
                1661-7827
                1660-4601
                16 June 2016
                June 2016
                : 13
                : 6
                : 599
                Affiliations
                [1 ]Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Science, Shenzhen University, Shenzhen 518060, China; lijc007@ 123456szu.edu.cn (J.Li); chencheng_sz@ 123456126.com (C.C.); jun.lu@ 123456aut.ac.nz (J.Lu)
                [2 ]School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1142, New Zealand
                Author notes
                [* ]Correspondence: bioaplei@ 123456szu.edu.cn (A.L.); huzl@ 123456szu.edu.cn (Z.H.); Tel.: +86-755-2653-5286 (A.L.); +86-755-2655-7244 (Z.H.)
                [†]

                These authors contributed equally to this work.

                Article
                ijerph-13-00599
                10.3390/ijerph13060599
                4924056
                27322295
                76d921bb-d274-419b-bebc-f2f9f55c6c68
                © 2016 by the authors; licensee MDPI, Basel, Switzerland.

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 18 April 2016
                : 08 June 2016
                Categories
                Article

                Public health
                bacterioplankton community composition (bcc),pcr-dgge,reservoir,trophic status
                Public health
                bacterioplankton community composition (bcc), pcr-dgge, reservoir, trophic status

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