Beyond the usual suspects: methanogenic communities in eastern North American peatlands are also influenced by nickel and copper concentrations

2021 ◽  
Author(s):  
Sydney E Bear ◽  
James D Seward ◽  
Louis Jamie Lamit ◽  
Nathan Basiliko ◽  
Tim Moore ◽  
...  
Keyword(s):  
Strong Predictor ◽  
Methanogenic Archaea ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Contaminated Sites ◽  
Methanogenic Community ◽  
Primary Driver ◽  
High Concentrations ◽  
Methyl Coenzyme M Reductase ◽  
Eastern Half

Abstract Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analyzed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands.

scholarly journals Archaeal and methanogenic communities in the rice field under different fertilizer applications

2019 ◽  
Vol 20 (12) ◽  
Author(s):  
Yuli Fatma ◽  
IMAN RUSMANA ◽  
ARIS TRI WAHYUDI ◽  
HAMIM
Keyword(s):  
Rice Field ◽  
Methanogenic Archaea ◽  
Archaeal Community ◽  
Amplicon Sequencing ◽  
Fertilizer Application ◽  
Emission Rates ◽  
Ch4 Emission ◽  
Dominant Group ◽  
Methanogenic Community ◽  
Growing Period

Abstract. Fatma YS, Rusmana I, Wahyudi AT, Hamim. 2019. Archaeal and methanogenic communities in the rice field under different fertilizer applications. Biodiversitas 20: 3667-3675. The archaeal community in the soil surrounding rice roots plays key roles in biogeochemical cycles. Methanogenic archaea contribute to CH4 production in the rice field and control CH4 emission rates; an important greenhouse gas significantly emitted from the rice field. Characteristic of archaeal and methanogenic community in Indonesian rice field has not been well documented. In this study, rice plants grown in the rice field were treated with two different fertilizer applications, i.e., 100% urea without biofertilizer (250 kg ha-1) (B0), and 50% urea (125 kg ha-1) with biofertilizer consisted of methanotrophic bacteria and N2O-reducing bacteria (B1). Soil archaeal community of the two types of fertilization was characterized over the rice-growing period using 16S rRNA amplicon sequencing. The succession and dynamic of the archaeal population were detected in each of the two treatments before fertilizer application (0 days after transplanting [DAT]) until the rice generative phase (69 DAT). During the period, the archaeal soil community in both treatments was dominated by Crenarchaeota. The relative abundance of putative methanogens was higher in the B0 treatment than that of B1 treatment. Within the methanogenic community, Methanosarcinaceae and Methanomassiliicoccaceae which found as most dominant group in both treatments were presumably to be important contributors to CH4 emission. The application of 50% urea with biofertilizer (B1) changed the structure of the archaeal and methanogenic community in the rice field compared to the application of 100% urea (B0).

Lysozyme Treatment Makes 16S rRNA Amplicon Sequencing Results Less Biased

2021 ◽  
Author(s):  
Yuting Jiao ◽  
Zijie Gao ◽  
Shiyu Gui ◽  
Lu Ren ◽  
Yongyue Lu ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis ◽  
Effective Agent ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
16S Rrna Amplicon Sequencing ◽  
Structure Result ◽  
Total Bacteria

Abstract Background Amplicon sequencing is widely applied in gut bacteria structure analysis. However, the proportion of Gram-positive bacteria may greatly affect the results of microbial community analysis. Lysozyme is an effective agent to extract DNA of Gram-positive bacteria. In this study, we assessed the influence of lysozyme treatment on results of Bactrocere dorsalis rectal bacteria structure. Result The results indicated that the total bacteria content can be significantly increased in lysozyme treated samples. Moreover, rectal bacteria diversity was significantly higher in lysozyme treated samples. A detail analysis revealed that abundance of Gram-positive bacteria significantly increased in samples treated with lysozyme. Conclusion This study indicates that lysozyme treatment before DNA extraction is an effective way to reduce bias in bacteria structure analysis, especially for samples with high proportion of Gram-positive bacteria.

scholarly journals Evaluation of sediment contamination by trace elements and the zooplankton community analysis in area affected by gold exploration in Southeast (SE) of the Iron Quadrangle, Alto Rio Doce, (MG) Brazil

2013 ◽  
Vol 25 (2) ◽  
pp. 150-157
Author(s):  
Cláudia de Lima e Silva ◽  
Adivane Terezinha da Costa ◽  
Giovanni Guimarães Landa ◽  
Herton Fabrício Camargos Fonseca ◽  
Aléssio Silveira
Keyword(s):  
Trace Elements ◽  
Reference Values ◽  
Zooplankton Community ◽  
Reference Value ◽  
Community Analysis ◽  
Major And Trace Elements ◽  
Geochemical Composition ◽  
Gold Exploration ◽  
Local Reference ◽  
High Concentrations

AIM: The aim was to verify the geochemical composition of sediments samples (riverbed and bank) and the relationship of the following elements: Al, As, Cd. Cr, Cu, Fe, Mn, Ni and Zn with the zooplankton community. METHODS: Bank and riverbed sediments were collected in four sampling points along the studied area, in June/2010 (dry season) and March/2011 (rainy season). Three types of analysis were performed: granulometric, mineralogical (by X-Ray diffractometer) and geochemical (by ICPOES), where for the last two types, only a fraction of silt/clay (<0.062 mm) was used, and the results were compared with the following reference values: Local Reference Value (Costa et al., 2010), Quality Reference Values (São Paulo, 2005), PEC and TEC values (MacDonald et al., 2000). For identification of the zooplankton community, riverbed and bank samples were collected in polyethylene bottles, suspended with deionized water (bank sample only), stained with Rose Bengal and preserved in formalin at 4%. RESULTS: As concentrations at Col sampled point were 18 times greater than the Local Reference Value (3.84 mg.kg-1). Cd concentrations were greater than the values established by the QRV (<0.5 mg.kg-1) and PEC (4.98 mg.kg-1) in almost all the sampled points, regarding seasonality. The following zooplanktonic species were identified: Arcella costata (Ehrenberg, 1847), Arcella discoides (Ehrenberg, 1843), Arcella vulgaris (Ehrenberg, 1830), Centropyxis aculeata (Ehrenberg, 1838), Centropyxis ecornis (Ehrenberg, 1841), Difflugia sp., Difflugia acuminata (Ehrenberg, 1838), Euglypha laevis (Perty, 1849), Trynema enchelys (Ehrenberg, 1938), Asplanchna priodonta (Gosse, 1850), and Bedelloida, with, approximately 81% belonging to the Protozoa group. CONCLUSIONS: The studied area, with the exception of the Tripuí point, was found to be impacted by historical gold exploration in the region, as well as by the growing urbanization. Within the elements considered to be the most toxic to the biota, As and Cd violated all their reference values. In spite of high concentrations of major and trace elements encountered at downstream points, testacea species were identified, suggesting that this group has the capacity to adapt to adverse situations.

scholarly journals Effects of Ectomycorrhizal Fungi and Heavy Metals (Pb, Zn, and Cd) on Growth and Mineral Nutrition of Pinus halepensis Seedlings in North Africa

2020 ◽  
Vol 8 (12) ◽  
pp. 2033
Author(s):  
Chadlia Hachani ◽  
Mohammed S. Lamhamedi ◽  
Claudio Cameselle ◽  
Susana Gouveia ◽  
Abdenbi Zine El Abidine ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
North Africa ◽  
Mineral Nutrition ◽  
Contaminated Soils ◽  
Mycorrhizal Fungi ◽  
Pinus Halepensis ◽  
Translocation Factor ◽  
Contaminated Sites ◽  
High Concentrations

The pollution of soils by heavy metals resulting from mining activities is one of the major environmental problems in North Africa. Mycorrhizoremediation using mycorrhizal fungi and adapted plant species is emerging as one of the most innovative methods to remediate heavy metal pollution. This study aims to assess the growth and the nutritional status of ectomycorrhizal Pinus halepensis seedlings subjected to high concentrations of Pb, Zn, and Cd for possible integration in the restoration of heavy metals contaminated sites. Ectomycorrhizal and non-ectomycorrhizal P. halepensis seedlings were grown in uncontaminated (control) and contaminated soils for 12 months. Growth, mineral nutrition, and heavy metal content were assessed. Results showed that ectomycorrhizae significantly improved shoot and roots dry masses of P. halepensis seedlings, as well as nitrogen shoot content. The absorption of Pb, Zn, and Cd was much higher in the roots than in the shoots, and significantly more pronounced in ectomycorrhizal seedlings—especially for Zn and Cd. The presence of ectomycorrhizae significantly reduced the translocation factor of Zn and Cd and bioaccumulation factor of Pb and Cd, which enhanced the phytostabilizing potential of P. halepensis seedlings. These results support the use of ectomycorrhizal P. halepensis in the remediation of heavy metal contaminated sites.

scholarly journals Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

2019 ◽  
Vol 116 (11) ◽  
pp. 5037-5044 ◽  
Author(s):  
Bojk A. Berghuis ◽  
Feiqiao Brian Yu ◽  
Frederik Schulz ◽  
Paul C. Blainey ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
Paradigm Shift ◽  
Carbon Fixation ◽  
Methanogenic Archaea ◽  
Global Carbon Cycle ◽  
Hydrogenotrophic Methanogenesis ◽  
Shared Ancestry ◽  
Hydrogenotrophic Methanogens ◽  
Methyl Coenzyme M Reductase ◽  
Global Carbon ◽  
Insight Into

Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-CoA [Wood–Ljungdahl pathway (WLP)], which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota, which we have named Candidatus Methanohydrogenales, as well as the presence of the WLP in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methylotrophic methanogenesis might have occurred.

scholarly journals Dynamics of the Methanogenic Archaea in Tropical Estuarine Sediments

Archaea ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
María del Rocío Torres-Alvarado ◽  
Francisco José Fernández ◽  
Florina Ramírez Vives ◽  
Francisco Varona-Cordero
Keyword(s):  
Organic Carbon ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Coastal Lagoons ◽  
Spatial Dynamics ◽  
Methanogenic Archaea ◽  
Estuarine Sediments ◽  
Microbiological Analysis ◽  
Methanogenic Community ◽  
Solids Content

Methanogenesis may represent a key process in the terminal phases of anaerobic organic matter mineralization in sediments of coastal lagoons. The aim of the present work was to study the temporal and spatial dynamics of methanogenic archaea in sediments of tropical coastal lagoons and their relationship with environmental changes in order to determine how these influence methanogenic community. Sediment samples were collected during the dry (February, May, and early June) and rainy seasons (July, October, and November). Microbiological analysis included the quantification of viable methanogenic archaea (MA) with three substrates and the evaluation of kinetic activity from acetate in the presence and absence of sulfate. The environmental variables assessed were temperature, pH, Eh, salinity, sulfate, solids content, organic carbon, and carbohydrates. MA abundance was significantly higher in the rainy season (106–107 cells/g) compared with the dry season (104–106 cells/g), with methanol as an important substrate. At spatial level, MA were detected in the two layers analyzed, and no important variations were observed either in MA abundance or activity. Salinity, sulfate, solids, organic carbon, and Eh were the environmental variables related to methanogenic community. A conceptual model is proposed to explain the dynamics of the MA.

scholarly journals Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Liyou Wu ◽  
Chongqing Wen ◽  
Yujia Qin ◽  
Huaqun Yin ◽  
Qichao Tu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Analysis ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis

Anaerobic methanethiol degradation and methanogenic community analysis in an alkaline (pH 10) biological process for liquefied petroleum gas desulfurization

2008 ◽  
Vol 101 (4) ◽  
pp. 691-701 ◽  
Author(s):  
Robin C. van Leerdam ◽  
Monica Bonilla-Salinas ◽  
Frank A.M. de Bok ◽  
H. Bruning ◽  
Piet N.L. Lens ◽  
...  
Keyword(s):  
Biological Process ◽  
Community Analysis ◽  
Alkaline Ph ◽  
Liquefied Petroleum Gas ◽  
Methanogenic Community

scholarly journals Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales

2017 ◽  
Vol 199 (16) ◽  
Author(s):  
Tristan Wagner ◽  
Carl-Eric Wegner ◽  
Jörg Kahnt ◽  
Ulrich Ermler ◽  
Seigo Shima
Keyword(s):  
Active Site ◽  
Phylogenetic Analyses ◽  
Methanogenic Archaea ◽  
Methane Formation ◽  
Type I ◽  
Type Ii ◽  
Coenzyme M ◽  
Content Type ◽  
Type Iii ◽  
Methyl Coenzyme M Reductase

ABSTRACT The phylogenetically diverse family of methanogenic archaea universally use methyl coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders Methanobacteriales and Methanococcales contain two isoenzymes. Comprehensive phylogenetic analyses on the basis of all three subunits grouped MCRs from Methanobacteriales and Methanococcales into three distinct types: (i) MCRs from Methanobacteriales, (ii) MCRs from Methanobacteriales and Methanococcales, and (iii) MCRs from Methanococcales. The first and second types contain MCR isoenzymes I and II from Methanothermobacter marburgensis, respectively; therefore, they were designated MCR type I and type II and accordingly; the third one was designated MCR type III. For comparison with the known MCR type I and type II structures, we determined the structure of MCR type III from Methanotorris formicicus and Methanothermococcus thermolithotrophicus. As predicted, the three MCR types revealed highly similar overall structures and virtually identical active site architectures reflecting the chemically challenging mechanism of methane formation. Pronounced differences were found at the protein surface with respect to loop geometries and electrostatic properties, which also involve the entrance of the active-site funnel. In addition, the C-terminal end of the γ-subunit is prolonged by an extra helix after helix γ8 in MCR type II and type III, which is, however, differently arranged in the two MCR types. MCR types I, II, and III share most of the posttranslational modifications which appear to fine-tune the enzymatic catalysis. Interestingly, MCR type III lacks the methyl-cysteine but possesses in subunit α of M. formicicus a 6-hydroxy-tryptophan, which thus far has been found only in the α-amanitin toxin peptide but not in proteins. IMPORTANCE Methyl coenzyme M reductase (MCR) represents a prime target for the mitigation of methane releases. Phylogenetic analyses of MCRs suggested several distinct sequence clusters; those from Methanobacteriales and Methanococcales were subdivided into three types: MCR type I from Methanobacteriales, MCR type II from Methanobacteriales and Methanococcales, and the newly designated MCR type III exclusively from Methanococcales. We determined the first X-ray structures for an MCR type III. Detailed analyses revealed substantial differences between the three types only in the peripheral region. The subtle modifications identified and electrostatic profiles suggested enhanced substrate binding for MCR type III. In addition, MCR type III from Methanotorris formicicus contains 6-hydroxy-tryptophan, a new posttranslational modification that thus far has been found only in the α-amanitin toxin.

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