Browsing by Author "Gu, Ji-Dong"

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A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples
(2013-12-01)
Han, Ping
;
Huang, Yu-Tzu
;
Lin, Jih-Gaw
;
Gu, Ji-Dong
;
環境工程研究所
Two 16S rRNA gene-based PCR primer sets (Brod541F/Amx820R and A438f/A684r) for detecting anammox bacteria were compared using sediments from Mai Po wetlands (MP), the South China Sea (SCS), a freshwater reservoir (R2), and sludge granules from a wastewater treatment plant (A2). By comparing their ability in profiling anammox bacteria, the recovered diversity, community structure, and abundance of anammox bacteria among all these diverse samples indicated that A438f/A684r performed better than Brod541F/Amx820R in retrieving anammox bacteria from these different environmental samples. Five Scalindua subclusters (zhenghei-I, SCS-I, SCS-III, arabica, and brodae) dominated in SCS whereas two Scalindua subclusters (zhenghei-II and wagneri) and one cluster of Kuenenia dominated in MP. R2 showed a higher diversity of anammox bacteria with two new retrieved clusters (R2-New-1 and R2-New-2), which deserves further detailed study. The dominance of Brocadia in sample A2 was supported by both of the primer sets used. Results collectively indicate strongly niche-specific community structures of anammox bacteria in different environments, and A438f/A684r is highly recommended for screening anammox bacteria from various environments when dealing with a collection of samples with diverse physiochemical characteristics.
A xylan-degrading thermophilic and obligate anaerobe Xylanivirga thermophila gen. nov., sp. nov., isolated from an anammox dominant wastewater treatment plant, and proposal of Xylanivirgaceae fam. nov.
(2020-02-01)
Liu, Lan
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Lv, Ai-Ping
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Ming, Yu-Zhen
;
Jiao, Jian-Yu
;
Xiao, Min
In our search for novel anaerobes with potential carbohydrate polymers degrading activity, we have isolated a xylan-degrading bacterial strain SYSU GA17129(T) from an anammox bacteria dominant wastewater treatment plant. Phylogenetic analysis of the 16S rRNA gene sequence indicated the strain SYSU GA17129(T) belong to the order Clostridiales and shared highest sequence identity with Caldicoprobacter faecalis DSM 20678(T) (89.9%). The strain was thermophilic, obligately anaerobic, non-motile and rod shaped. Optimum growth of the strain was observed at 45 degrees C, pH 8.0 and in the presence of 0.5% NaCl (w/v). The chemotaxonomic features of the strain SYSU GA17129(T) comprised of C-14:0 FAME, iso-C-15:0 FAME and C-16:0 FAME as the major fatty acids (>10%), diphosphatidylglycerol, phosphatidylinositol mannoside, an unidentified phospholipid, three unidentified polar lipids and two unidentified glycolipids as its polar lipids, and meso-diaminopimelic acid (meso-DAP) as the diamino acid in peptidoglycan. The G + C content of the genomic DNA was 35.9%. The strain could be distinguished from other defined families within the order Clostridiales by the differences in phenotypic and physiological characteristics, distinct phylogenetic lineage in 16S rRNA gene- and genome-based phylogenies and low genomic relatedness index. Based on these distinguishing properties, strain SYSU GA17129(T) is proposed to represent a new species of a new genus Xylanivirga thermophila gen. nov., sp. nov., within a new family Xylanivirgaceae fam. nov. The type species of the new taxon is SYSU GA17129(T) (=KCTC 15754(T) = CGMCC 1.5282(T)). This strain is characterized within the order Clostridiales, class Clostridia of the phylum Firmicutes. (C) 2019 Elsevier Ltd. All rights reserved.
Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems
(2020-03-01)
Yang, Yuchun
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Daims, Holger
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Liu, Yang
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Herbold, Craig W.
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Pjevac, Petra
The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions. IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.
Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA and functional genes
(2017-10-01)
Han, Ping
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Kluemper, Uli
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Wong, Alex
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Li, Meng
;
Lin, Jih-Gaw
Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd(1)-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples. WWTP had the lowest diversity with Candidatus Kuenenia dominating while the SCS was dominated by Candidatus Scalindua. MP showed the highest diversity of anammox bacteria including C. Scalindua, C. Kuenenia, and Candidatus Brocadia. Comparing different primer sets, no significant differences in specificity for 16S rRNA gene could be distinguished. Primer set CL1 showed relatively high efficiency in detecting the anammox bacterium hzo gene from all samples, while CL2 showed greater selectivity for WWTP samples. The recently reported primer sets of the hzsA gene resulted in high efficiencies in detecting anammox bacteria while nirS primer sets were more selective for specific samples. Results collectively indicate that the distribution of anammox bacteria is niche-specific within different ecosystems and primer specificity may cause biases on the diversity detected.
Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments
(2016-12)
Chen, Jing
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Dick, Richard
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Lin, Jih-Gaw
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Gu, Ji-Dong
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環境工程研究所
Nitrite-dependent anaerobic methane oxidation (n-damo) process uniquely links microbial nitrogen and carbon cycles. Research on n-damo bacteria progresses quickly with experimental evidences through enrichment cultures. Polymerase chain reaction (PCR)-based methods for detecting them in various natural ecosystems and engineered systems play a very important role in the discovery of their distribution, abundance, and biodiversity in the ecosystems. Important characteristics of n-damo enrichments were obtained and their key significance in microbial nitrogen and carbon cycles was investigated. The molecular methods currently used in detecting n-damo bacteria were comprehensively reviewed and discussed for their strengths and limitations in applications with a wide range of samples. The pmoA gene-based PCR primers for n-damo bacterial detection were evaluated and, in particular, several incorrectly stated PCR primer nucleotide sequences in the published papers were also pointed out to allow correct applications of the PCR primers in current and future investigations. Furthermore, this review also offers the future perspectives of n-damo bacteria based on current information and methods available for a better acquisition of new knowledge about this group of bacteria.
Insights into the roles of anammox bacteria in post-treatment of anaerobically-treated sewage
(2018-01-01)
Wang, Qian
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Tan, Giin-Yu Amy
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Azari, Mohammad
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Huang, Xiaowu
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Denecke, Martin
Complete anaerobic treatment of sewage has the potential to achieve net energy production via capturing the energy of organics in sewage, but not nitrogen, which remains a concern. Anaerobic ammonium oxidation (anammox) is potential for energy-efficient nitrogen removal from anaerobically-treated sewage. Given the sensitivity of anammox bacteria and the challenge of the low ammonium-bearing influent with reduced compounds such as volatile fatty acids, methane, and sulfide, this article critically reviewed and analyzed, using thermodynamic computation as a tool, the potential interactions of anammox bacteria with other microbes induced by the reduced compounds in anaerobically-treated sewage. The dynamics of anammox bacteria to cooperate with these microbes that metabolize non-ammonium pollutants and to outcompete for the common substrate, i.e., nitrite, are extensively discussed. The versatile metabolism of anammox bacteria on volatile fatty acids and iron, which would help facilitate the treatment efficiency, was also reviewed. The information offered in this review will be beneficial to researchers and engineers in controlling process stability, enhancing total nitrogen removal, and achieving better effluent quality in post-treatment of anaerobically-treated sewage by anammox-based processes.
Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge
(2019-08-01)
Liu, Zongbao
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Klumper, Uli
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Liu, Yang
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Yang, Yuchun
;
Wei, Qiaoyan
Wastewater treatment plants (WWTPs) are a source and reservoir for subsequent spread of various antibiotic resistance genes (ARGs). However, little is known about the activity and hosts of ARGs in WWTPs. Here, we utilized both metagenomic and metatranscriptomic approaches to comprehensively reveal the diversity, abundance, expression and hosts of ARGs in activated sludge (AS) from three conventional WWTPs in Taiwan. Based on deep sequencing data and a custom-made ARG database, a total of 360 ARGs associated with 24 classes of antibiotics were identified from the three AS metagenomes, with an abundance range of 7.06 x 10(-1)-1.20 x 10(-4) copies of ARG/copy of 16S rRNA gene. Differential coverage binning analysis revealed that > 22 bacterial phyla were the putative hosts of the identified ARGs. Surprisingly, genus Mycobacterium and family Burkholderiaceae were observed as multi-drug resistant harboring 14 and 50 ARGs. Metatranscriptome analysis showed 65.8% of the identified ARGs were being expressed, highlighting that ARGs were not only present, but also transcriptionally active in AS. Remarkably, 110 identified ARGs were annotated as plasmid-associated and displayed a close to two-fold increased likelihood of being transcriptionally expressed compared to those ARGs found exclusively within bacterial chromosomes. Further analysis showed the transcript abundance of aminoglycoside, sulfonamide, and tetracycline resistance genes was mainly contributed by plasmid-borne ARGs. Our approach allowed us to specifically link ARGs to their transcripts and genetic context, providing a comprehensive insight into the prevalence, expression and hosts of ARGs in AS. Overall, results of this study enhance our understanding of the distribution and dissemination of ARGs in WWTPs, which benefits environmental risk assessment and management of ARB and ARGs.
Occurrence of anammox bacteria in a traditional full-scale wastewater treatment plant and successful inoculation for new establishment
(2017-05-01)
Meng, Han
;
Yang, Yu-Chun
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Lin, Jih-Gaw
;
Denecke, Martin
;
Gu, Ji-Dong
A new biochemical pathway for reactive nitrogen removal from wastewater has been recognized as anaerobic ammonium oxidation (anammox) since its first discovery in the 1990's. Over the past decades, many studies have been focused on laboratory scale reactors for enrichment of the anammox bacteria for potential applications on an industrial scale. The research reported here investigated the occurrence, community diversity and abundance of anammox bacteria observed for the first time in a full-scale wastewater treatment plant (Plant N) in Taiwan and then successful inoculation of the initially enriched anammox bacteria granules into another full-scale wastewater treatment plant (Plant S). The community composition was similar in both plants, showing similarity in the existence of Ca. Brocadia as the dominating genus of anammox bacteria. Inoculation of the existing sludge containing active anammox bacteria into other plant resulted in an effective establishment of anammox bacteria in as little as 6 months in a full-scale wastewater treatment plant. The abundance of anammox bacteria was significantly different between these two plants with the newly inoculated one containing 2 to 100 times higher gene copies of the anammox bacteria than Plant N serving as an inoculum. In addition, differences were also observed between the sludge and immobilizing carrier materials, which supported the colonization of anammox bacteria and retained them to reach to a much high density in the wastewater treatment system. Based on qPCR results and TEM observation, anammox bacteria in those treatment plants were active and contributed to inorganic N removal. The inoculation study showed that anammox process can be activated without re-design of the system and inoculation was successful to activate anammox process effectively to achieve the inorganic N removal in conventional wastewater treatment plants. (C) 2017 Elsevier Ltd. All rights reserved.
Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes
(2020-09-10)
Yang, Yuchun
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Li, Meng
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Li, Hui
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Li, Xiao-Yan
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Lin, Jih-Gaw