Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals

2016 ◽  
Vol 74 (4) ◽  
pp. 824-835 ◽  
Author(s):  
Janet Jiménez ◽  
Susanne Theuerl ◽  
Ingo Bergmann ◽  
Michael Klocke ◽  
Gilda Guerra ◽  
...  

The aim of this study was to analyze the effect of the addition of rice straw and clay residuals on the prokaryote methane-producing community structure in a semi-continuously stirred tank reactor fed with swine manure. Molecular techniques, including terminal restriction fragment length polymorphism and a comparative nucleotide sequence analyses of the prokaryotic 16S rRNA genes, were performed. The results showed a positive effect of clay addition on methane yield during the co-digestion of swine manure and rice straw. At the digestion of swine manure, the bacterial phylum Firmicutes and the archaeal family Methanosarcinaceae, particularly Methanosarcina species, were predominant. During the co-digestion of swine manure and rice straw the microbial community changed, and with the addition of clay residual, the phylum Bacteroidetes predominated. The new nutritional conditions resulted in a shift in the archaeal family Methanosarcinaceae community as acetoclastic Methanosaeta species became dominant.

Archaea ◽  
2005 ◽  
Vol 1 (6) ◽  
pp. 391-397 ◽  
Author(s):  
Atsuo Sugano ◽  
Hidetaka Tsuchimoto ◽  
Tun Cho Cho ◽  
Makoto Kimura ◽  
Susumu Asakawa

The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related toMethanomicrobialesand Rice cluster I.Methanomicrobiales, Rice cluster I andMethanosarcinaleswere major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related toMethanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.


2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S492-S492
Author(s):  
David C Nguyen ◽  
Michelle Lisgaris ◽  
Sruthi Vasireddy ◽  
Richard J Wallace ◽  
Federico Perez ◽  
...  

Abstract Background The widespread use of molecular techniques has resulted in increasing numbers of newly characterized rapidly growing mycobacteria (RGM). Many RGM cause soft tissue and orthopedic hardware infection, particularly after trauma. RGM species identification remains challenging with few genetic differences between species. Methods We describe a case involving RGM. We report results of matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (Bruker Biotyper), sequencing of rpoB, erm(39), and 16S rRNA genes, and antibiotic susceptibility testing (AST). We review previous reports describing similar RGM infections. Results A 58-year-old male sustained multiple fractures and right thigh compartment syndrome after a motorcycle accident. He underwent fasciotomy and multi-stage surgical fixations. 3 months later, he had wound dehiscence, purulence and multiple fluid collections of his right leg and knee requiring surgical drainage and removal of orthopedic hardware. After 4 days, acid-fast bacilli grew on routine bacterial culture media. MALDI-TOF identified the isolate as Mycobacterium mageritense. In contrast, sequencing of 16S rRNA (100% identity) and erm(39) (> 99% identity) identified the isolate as Mycobacterium houstonense; erm(39) only had 80% similarity with Mycobacterium fortuitum. Sequencing of rpoB showed a 19 bp difference with the M. houstonense type strain, and showed similarity to M. fortuitum (97.64%) than M. houstonense (97.45%). AST demonstrated resistance to clarithromycin only. After initial treatment with imipenem, ciprofloxacin, and doxycycline, definite therapy with ciprofloxacin and doxycycline was successful. In the literature, we found one case each of M. mageritense and M. houstonense infection after trauma. Conclusion This case highlights the importance of RGM other than M. fortuitum as a cause of soft tissue and orthopedic hardware infections, and illustrates the difficulty of identifying them to the species level. Sequencing of erm(39) and 16S rRNA gene identified the isolate as M. houstonense, but the larger difference (>2.5%) in rpoB sequence suggests a novel species. Further characterization is underway. Efforts to determine RGM species and antibiotic susceptibility give important insight into diagnosis and management. Disclosures All authors: No reported disclosures.


2006 ◽  
Vol 53 (8) ◽  
pp. 139-147 ◽  
Author(s):  
B. Calli ◽  
S. Durmaz ◽  
B. Mertoglu

To identify the microbial communities in Istanbul, Odayeri Municipal Solid Waste Landfill, leachate samples were collected from different sections at different stabilization phases. In identification of microbial communities in leachate samples, molecular techniques such as FISH, DGGE and cloning based on 16S rRNA and mcrA genes were used. As the chemical and microbiological compositions of the samples were compared, obvious correlations were found between the stability of the landfill section and abundance of active methanogens. On the other hand, there were considerable differences between acidogenic and mature leachate samples in DGGE profiles of archaeal and bacterial 16S rRNA genes. Moreover, in acidogenic leachate samples having BOD5/COD ratio of about 0.5 acetate utilizing Methanosarcina and Methanosaeta species were intensively detected in FISH. Although only very few H2-utilizing methanogens were identified with FISH analysis, most of the clones isolated from mature leachate samples clustered within H2-utilizing Methanobacteriales and Methanomicrobiales according to phylogenetic analysis of 16S rRNA and mcrA clones, respectively.


Archaea ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-14
Author(s):  
Wei-Yu Chen ◽  
Lucia Kraková ◽  
Jer-Horng Wu ◽  
Domenico Pangallo ◽  
Lenka Jeszeová ◽  
...  

Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS) and an upflow anaerobic sludge blanket (UASB) reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenicarchaeawere highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed thatMethanomethylovoransandMethanosarcinawere the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of oneMethanomethylovoranspopulation in the CMSS reactor, diverse methylotrophicMethanosarcinaspecies inhabited in syntrophy-like association with hydrogenotrophicMethanobacteriumin the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application.


2017 ◽  
Vol 66 (1) ◽  
pp. 39-56
Author(s):  
Nilgun Tekin ◽  
Arzu Coleri Cihan ◽  
Basar Karaca ◽  
Cumhur Cokmus

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.


Acta Naturae ◽  
2012 ◽  
Vol 4 (4) ◽  
pp. 91-97 ◽  
Author(s):  
A. M. Ziganshin ◽  
E. E. Ziganshina ◽  
S. Kleinsteuber ◽  
J. Pröter ◽  
O. N. Ilinskaya

This work is devoted to the investigation of the methanogenic archaea involved in anaerobic digestion of cattle manure and maize straw on the basis of terminal restriction fragment length polymorphism (TRFLP) analysis of archaeal 16S rRNA genes. The biological diversity and dynamics of methanogenic communities leading to anaerobic degradation of agricultural organic wastes with biogas production were evaluated in laboratory-scale digesters. T-RFLP analysis, along with the establishment of archaeal 16S rRNA gene clone libraries, showed that the methanogenic consortium consisted mainly of members of the genera Methanosarcina and Methanoculleus, with a predominance of Methanosarcina spp. throughout the experiment.


2008 ◽  
Vol 57 (12) ◽  
pp. 1569-1576 ◽  
Author(s):  
Tanja Kuehbacher ◽  
Ateequr Rehman ◽  
Patricia Lepage ◽  
Stephan Hellmig ◽  
Ulrich R. Fölsch ◽  
...  

TM7 is a recently described subgroup of Gram-positive uncultivable bacteria originally found in natural environmental habitats. An association of the TM7 bacterial division with the inflammatory pathogenesis of periodontitis has been previously shown. This study investigated TM7 phylogenies in patients with inflammatory bowel diseases (IBDs). The mucosal microbiota of patients with active Crohn's disease (CD; n=42) and ulcerative colitis (UC; n=31) was compared with that of controls (n=33). TM7 consortia were examined using molecular techniques based on 16S rRNA genes, including clone libraries, sequencing and in situ hybridization. TM7 molecular signatures could be cloned from mucosal samples of both IBD patients and controls, but the composition of the clone libraries differed significantly. Taxonomic analysis of the sequences revealed a higher diversity of TM7 phylotypes in CD (23 different phylotypes) than in UC (10) and non-IBD controls (12). All clone libraries showed a high number of novel sequences (21 for controls, 34 for CD and 29 for UC). A highly atypical base substitution for bacterial 16S rRNA genes associated with antibiotic resistance was detected in almost all sequences from CD (97.3 %) and UC (100 %) patients compared to only 65.1 % in the controls. TM7 bacteria might play an important role in IBD similar to that previously described in oral inflammation. The alterations of TM7 bacteria and the genetically determined antibiotic resistance of TM7 species in IBD could be a relevant part of a more general alteration of bacterial microbiota in IBD as recently found, e.g. as a promoter of inflammation at early stages of disease.


2000 ◽  
Vol 42 (3-4) ◽  
pp. 143-148 ◽  
Author(s):  
S.J. You ◽  
C.F. Ouyang ◽  
S.F. Lin ◽  
W.T. Liu

Molecular techniques were used to compare the microbial community of suspended activated sludge and attached biofilm in a biological nutrient removal process (TNCU-I) operated under various COD/total P (COD/TP) feed ratios. Analysis of restriction fragment length polymorphism of amplified 16S rRNA genes indicated that the microbial population structures were more closely related among those sludge samples taken from aerobic sludge than that taken from biofilm attached on the RBC. The use of different COD/TP feed ratios (300/2.5-300/25) had no significant effect on the change of microbial structures of sludge samples. The 16S rDNA clone library further indicated that at least eight and six different microbial populations were present in activated sludge and RBC biofilm, respectively. The phylogenetic analysis revealed that six of those eight major clones obtained from the suspended activated sludge were from the beta-subclass of the class Proteobacteria. In contrast, only one clone obtained from biofilm belonged to the beta-subclass of the Proteobacteria. This difference in the microbial population structure was possibly attributed to the growth state (suspended or attached) or carbon source (autographs or heterotrophs) of the sludge samples rather than the effect of the COD/TP ratio used.


mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Victoria E. MeGraw ◽  
Ashley R. Brown ◽  
Christopher Boothman ◽  
Royston Goodacre ◽  
Katherine Morris ◽  
...  

ABSTRACTGeochemical analyses alongside molecular techniques were used to characterize the microbial ecology and biogeochemistry of an outdoor spent nuclear fuel storage pond at Sellafield, United Kingdom, that is susceptible to seasonal algal blooms that cause plant downtime. 18S rRNA gene profiling of the filtered biomass samples showed the increasing dominance of a species closely related to the algaHaematococcus pluvialis, alongside 16S rRNA genes affiliated with a diversity of freshwater bacteria, includingProteobacteriaandCyanobacteria. High retention of137Cs and90Sr on pond water filters coincided with high levels of microbial biomass in the pond, suggesting that microbial colonization may have an important control on radionuclide fate in the pond. To interpret the unexpected dominance ofHaematococcusspecies during bloom events in this extreme environment, the physiological response ofH. pluvialisto environmentally relevant ionizing radiation doses was assessed. Irradiated laboratory cultures produced significant quantities of the antioxidant astaxanthin, consistent with pigmentation observed in pond samples. Fourier transform infrared (FT-IR) spectroscopy suggested that radiation did not have a widespread impact on the metabolic fingerprint ofH. pluvialisin laboratory experiments, despite the 80-Gy dose. This study suggests that the production of astaxanthin-rich encysted cells may be related to the preservation of theHaematococcusphenotype, potentially allowing it to survive oxidative stress arising from radiation doses associated with the spent nuclear fuel. The oligotrophic and radiologically extreme conditions in this environment do not prevent extensive colonization by microbial communities, which play a defining role in controlling the biogeochemical fate of major radioactive species present.IMPORTANCESpent nuclear fuel is stored underwater in large ponds prior to processing and disposal. Such environments are intensively radioactive but can be colonized by microorganisms. Colonization of such inhospitable radioactive ponds is surprising, and the survival mechanisms that microbes use is of fundamental interest. It is also important to study these unusual ecosystems, as microbes growing in the pond waters may accumulate radionuclides present in the waters (for bioremediation applications), while high cell loads can hamper management of the ponds due to poor visibility. In this study, an outdoor pond at the U.K. Sellafield facility was colonized by a seasonal bloom of microorganisms, able to accumulate high levels of137Cs and90Sr and dominated by the algaHaematococcus. This organism is not normally associated with deep water bodies, but it can adapt to radioactive environments via the production of the pigment astaxanthin, which protects the cells from radiation damage.


2003 ◽  
Vol 69 (11) ◽  
pp. 6610-6619 ◽  
Author(s):  
Robin Brinkmeyer ◽  
Katrin Knittel ◽  
Jutta Jürgens ◽  
Horst Weyland ◽  
Rudolf Amann ◽  
...  

ABSTRACT A comprehensive assessment of bacterial diversity and community composition in arctic and antarctic pack ice was conducted through cultivation and cultivation-independent molecular techniques. We sequenced 16S rRNA genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively. Most of the 33 arctic phylotypes were >97% identical to previously described antarctic species or to our own antarctic isolates. At both poles, the α- and γ-proteobacteria and the Cytophaga-Flavobacterium group were the dominant taxonomic bacterial groups identified by cultivation as well as by molecular methods. The analysis of 16S rRNA gene clone libraries from multiple arctic and antarctic pack ice samples revealed a high incidence of closely overlapping 16S rRNA gene clone and isolate sequences. Simultaneous analysis of environmental samples with fluorescence in situ hybridization (FISH) showed that∼ 95% of 4′,6′-diamidino-2-phenylindole (DAPI)-stained cells hybridized with the general bacterial probe EUB338. More than 90% of those were further assignable. Approximately 50 and 36% were identified asγ -proteobacteria in arctic and antarctic samples,respectively. Approximately 25% were identified asα -proteobacteria, and 25% were identified as belonging to the Cytophaga-Flavobacterium group. For the quantification of specific members of the sea ice community, new oligonucleotide probes were developed which target the genera Octadecabacter, Glaciecola, Psychrobacter, Marinobacter, Shewanella, and Polaribacter. High FISH detection rates of these groups as well as high viable counts corroborated the overlap of clone and isolate sequences. A terrestrial influence on the arctic pack ice community was suggested by the presence of limnic phylotypes.


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