scholarly journals Effect of Afforestation and Reforestation of Pastures on the Activity and Population Dynamics of Methanotrophic Bacteria

2007 ◽  
Vol 73 (16) ◽  
pp. 5153-5161 ◽  
Author(s):  
Brajesh K. Singh ◽  
Kevin R. Tate ◽  
Gokul Kolipaka ◽  
Carolyn B. Hedley ◽  
Catriona A. Macdonald ◽  
...  
Keyword(s):  
Community Structure ◽  
Methane Oxidation ◽  
Phospholipid Fatty Acid ◽  
Pine Forest ◽  
Polymorphism Analysis ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Type Ii ◽  
Methylococcus Capsulatus ◽  
Methanotrophic Communities

ABSTRACT We investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different New Zealand sites. Methane oxidation was measured in soils from two pine (Pinus radiata) forests and one shrubland (mainly Kunzea ericoides var. ericoides) and three adjacent permanent pastures. The methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. A combination of phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of these soils revealed that different methanotrophic communities were active in soils under the different vegetations. The C18 PLFAs (signature of type II methanotrophs) predominated under pine and shrublands, and C16 PLFAs (type I methanotrophs) predominated under pastures. Analysis of the methanotrophs by molecular methods revealed further differences in methanotrophic community structure under the different vegetation types. Cloning and sequencing and terminal-restriction fragment length polymorphism analysis of the particulate methane oxygenase gene (pmoA) from different samples confirmed the PLFA-SIP results that methanotrophic bacteria related to type II methanotrophs were dominant in pine forest and shrubland, and type I methanotrophs (related to Methylococcus capsulatus) were dominant in all pasture soils. We report that afforestation and reforestation of pastures caused changes in methane oxidation by altering the community structure of methanotrophic bacteria in these soils.

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

Microbiology ◽  
2004 ◽  
Vol 150 (5) ◽  
pp. 1301-1313 ◽  
Author(s):  
Svetlana N. Dedysh ◽  
Peter Ricke ◽  
Werner Liesack
Keyword(s):  
16S Rrna ◽  
Amino Acid Sequences ◽  
Phenotypic Trait ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Type Ii ◽  
Methylococcus Capsulatus ◽  
Available Nitrogen ◽  
Active Growth ◽  
Nitrogen Acquisition

The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus Beijerinckia. To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98·5 and 96·6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition. This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M. acidiphila B2 and Beijerinckia spp. are capable of active growth on nitrogen-free media under fully aerobic conditions.

The Molecular Basis of Antithrombin Deficiency in Belgian and Dutch Families

1998 ◽  
Vol 80 (09) ◽  
pp. 376-381 ◽  
Author(s):  
W. Lissens ◽  
S. Seneca ◽  
P. Capel ◽  
B. Chatelain ◽  
P. Meeus ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Gene Deletion ◽  
Direct Sequencing ◽  
Genetic Defect ◽  
Polymorphism Analysis ◽  
Type I ◽  
Type Ii ◽  
Antithrombin Deficiency ◽  
Venous Thromboembolic Events ◽  
At Deficiency

SummaryThe molecular basis of hereditary antithrombin (AT) deficiency has been investigated in ten Belgian and three Dutch unrelated kindreds. Eleven of these families had a quantitative or type I AT deficiency, with a history of major venous thromboembolic events in different affected members. In the other two families a qualitative or type II AT deficiency was occasionally diagnosed.DNA studies of the AT gene were performed, using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) analysis, followed by direct sequencing of the seven exons and intronexon junction regions. Six novel point mutations were identified: four missense, one nonsense mutation and a single nucleotide deletion near the reactive site, causing a frameshift with premature translation termination. In two kindreds the underlying genetic defect was caused by a whole gene deletion, known as a rare cause of AT deficiency. In these cases, Southern blot and polymorphism analysis of different parts of the AT gene proved useful for diagnosis. In another kindred a partial gene deletion spanning 698 basepairs could precisely be determined to a part of intron 3B and exon 4. In two type I and in both type II AT deficient families a previously reported mutation was identified. In all cases, the affected individuals were heterozygous for the genetic defect.

scholarly journals Quantitative Detection of Methanotrophs in Soil by Novel pmoA-Targeted Real-Time PCR Assays

2003 ◽  
Vol 69 (5) ◽  
pp. 2423-2429 ◽  
Author(s):  
Steffen Kolb ◽  
Claudia Knief ◽  
Stephan Stubner ◽  
Ralf Conrad
Keyword(s):  
Community Structure ◽  
Real Time ◽  
Real Time Pcr ◽  
Pcr Analysis ◽  
Quantitative Detection ◽  
Methanotrophic Bacteria ◽  
Methylococcus Capsulatus ◽  
Α Subunit ◽  
Target Molecules ◽  
Pcr Assays

ABSTRACT Methane oxidation in soils is mostly accomplished by methanotrophic bacteria. Little is known about the abundance of methanotrophs in soils, since quantification by cultivation and microscopic techniques is cumbersome. Comparison of 16S ribosomal DNA and pmoA (α subunit of the particulate methane monooxygenase) phylogenetic trees showed good correlation and revealed five distinct groups of methanotrophs within the α and γ subclasses of Proteobacteria: the Methylococcus group, the Methylobacter/Methylosarcina group, the Methylosinus group, the Methylocapsa group, and the forest clones group (a cluster of pmoA sequences retrieved from forest soils). We developed quantitative real-time PCR assays with SybrGreen for each of these five groups and for all methanotrophic bacteria by targeting the pmoA gene. Detection limits were between 101 and 102 target molecules per reaction for all assays. Real-time PCR analysis of soil samples spiked with cells of Methylococcus capsulatus, Methylomicrobium album, and Methylosinus trichosporium recovered almost all the added bacteria. Only the Methylosinus-specific assay recovered only 20% of added cells, possibly due to a lower lysis efficiency of type II methanotrophs. Analysis of the methanotrophic community structure in a flooded rice field soil showed (5.0 ± 1.4) × 106 pmoA molecules g−1 for all methanotrophs. The Methylosinus group was predominant (2.7 × 106 ± 1.1 × 106 target molecules g−1). In addition, bacteria of the Methylobacter/Methylosarcina group were abundant (2.0 × 106 ± 0.9 × 106 target molecules g of soil−1). On the other hand, pmoA affiliated with the forest clones and the Methylocapsa group was below the detection limit of 1.9 × 104 target molecules g of soil−1. Our results showed that pmoA-targeted real-time PCR allowed fast and sensitive quantification of the five major groups of methanotrophs in soil. This approach will thus be useful for quantitative analysis of the community structure of methanotrophs in nature.

scholarly journals Soil microbial communities following bush removal in a Namibian savanna

2015 ◽  
Vol 2 (2) ◽  
pp. 1393-1418
Author(s):  
J. S. Buyer ◽  
A. Schmidt-Küntzel ◽  
M. Nghikembua ◽  
J. E. Maul ◽  
L. Marker
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Management Approach ◽  
Polymorphism Analysis ◽  
Soil Microbial

Abstract. Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

scholarly journals Wide Distribution of a Novel pmoA-Like Gene Copy among Type II Methanotrophs, and Its Expression in Methylocystis Strain SC2

2003 ◽  
Vol 69 (9) ◽  
pp. 5593-5602 ◽  
Author(s):  
Merlin Tchawa Yimga ◽  
Peter F. Dunfield ◽  
Peter Ricke ◽  
Jürgen Heyer ◽  
Werner Liesack
Keyword(s):  
Purifying Selection ◽  
Wide Distribution ◽  
Gene Copy ◽  
Northern Hybridization ◽  
Rrna Gene ◽  
Type I ◽  
Type Ii ◽  
Methylococcus Capsulatus ◽  
Reverse Transcription Pcr ◽  
Wide Range

ABSTRACT Experiments were conducted to determine if a novel pmoA-like gene (pmoA2) recently discovered in the methane-oxidizing bacterium Methylocystis strain SC2 (P. F. Dunfield, M. Tchawa Yimga, S. D. Dedysh, U. Berger, W. Liesack, and J. Heyer, FEMS Microbiol. Ecol. 41:17-26, 2002) is present in other methane-oxidizing bacteria (MOB), and if it is expressed. A newly developed primer combination (pmoA206f-pmoA703b) allowed a differential detection of pmoA1 and pmoA2. By using this primer combination, we identified pmoA2 in a wide range of type II MOB of the Methylosinus-Methylocystis group. However, screening by PCR and by Southern hybridization using a newly developed pmoA2-specific oligonucleotide probe also showed that closely related type II MOB, exhibiting 16S rRNA gene sequence identities of higher than 97%, may or may not harbor pmoA2. No pmoA2 was detected in five type I MOB tested: Methylococcus capsulatus strain Bath, Methylocaldum strain E10A, Methylobacter luteus, Methylomicrobium album, and Methylomonas strain D1a. In comparative sequence analyses, all pmoA2-like sequences formed a coherent cluster clearly distinct from pmoA1 sequences of type I and type II MOB, and from amoA sequences of the Nitrosomonas-Nitrosospira group. Phylogenetic analysis using the paml model suggested that pmoA2 is subject to strong purifying selection and therefore has an important cellular function. We probed total RNA extracts of Methylocystis strain SC2 for gene expression of pmoA. A strong signal was observed for pmoA1 in Northern hybridization, while the results obtained for pmoA2 were ambiguous. However, reverse transcription-PCR confirmed that pmoA2 was expressed, albeit at lower level than pmoA1. This provided experimental evidence that the gene product of pmoA2 may be a functionally active enzyme.

scholarly journals Soil microbial communities following bush removal in a Namibian savanna

SOIL ◽  
2016 ◽  
Vol 2 (1) ◽  
pp. 101-110 ◽  
Author(s):  
Jeffrey S. Buyer ◽  
Anne Schmidt-Küntzel ◽  
Matti Nghikembua ◽  
Jude E. Maul ◽  
Laurie Marker
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Management Approach ◽  
Polymorphism Analysis ◽  
Soil Microbial

Abstract. Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

scholarly journals A Morphological and Molecular Perspective of Trichoderma viride: Is It One or Two Species?

1999 ◽  
Vol 65 (6) ◽  
pp. 2418-2428 ◽  
Author(s):  
Elke Lieckfeldt ◽  
Gary J. Samuels ◽  
Helgard I. Nirenberg ◽  
Orlando Petrini
Keyword(s):  
Trichoderma Viride ◽  
Molecular Data ◽  
Molecular Characteristics ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Type I ◽  
28S Rrna ◽  
Type Ii ◽  
Species Type ◽  
Dna Pattern

ABSTRACT Trichoderma (Ascomycetes,Hypocreales) strains that have warted conidia are traditionally identified as T. viride, the type species ofTrichoderma. However, two morphologically distinct types of conidial warts (I and II) have been found. Because each type corresponds to a unique mitochondrial DNA pattern, it has been questioned whether T. viride comprises more than one species. Combined molecular data (sequences of the internal transcribed spacer 1 [ITS-1] and ITS-2 regions and of part of the 28S rRNA gene along with results of restriction fragment length polymorphism analysis of the endochitinase gene and PCR fingerprinting), morphology, physiology, and colony characteristics distinguish type I and type II as different species. Type I corresponds to “true” T. viride, the anamorph of Hypocrea rufa. Type II represents a new species, T. asperellum, which is, in terms of molecular characteristics, close to the neotype of T. hamatum.

Phospholipid fatty acid composition in type I and type II rat muscle

Lipids ◽  
1997 ◽  
Vol 32 (2) ◽  
pp. 193-198 ◽  
Author(s):  
William G. Blackard ◽  
Jing Li ◽  
John N. Clore ◽  
William B. Rizzo
Keyword(s):  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Phospholipid Fatty Acid ◽  
Type I ◽  
Phospholipid Fatty Acid Composition ◽  
Type Ii ◽  
Rat Muscle

scholarly journals Multiple groups of methanotrophic bacteria mediate methane oxidation in anoxic lake sediments

2021 ◽  
Author(s):  
Guangyi Su ◽  
Jakob Zopfi ◽  
Moritz F. Lehmann
Keyword(s):  
Lake Sediments ◽  
Methane Oxidation ◽  
Methane Emissions ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Anoxic Sediments ◽  
Anoxic Conditions ◽  
Aerobic Methanotrophs ◽  
Multiple Groups ◽  
Lake Sempach

Freshwater lakes represent an important source of the potent greenhouse gas methane (CH4) to the atmosphere. Methane emissions are regulated to large parts by aerobic (MOx) and anaerobic (AOM) oxidation of methane that are important sinks in lakes. In contrast to marine benthic environments, our knowledge about the modes of AOM and the related methanotrophic microorganisms in anoxic lake sediments is still rudimentary. Here we demonstrate the occurrence of AOM in the anoxic sediments of Lake Sempach (Switzerland), with maximum in situ AOM rates observed within the surface sediment layers in presence of multiple groups of methanotrophic bacteria and various oxidants known to support AOM. However, substrate-amended incubations (with NO2-, NO3-, SO42-, Fe3+ and Mn4+) revealed that none of the electron acceptors previously reported to support AOM enhanced methane turnover in Lake Sempach sediments under anoxic conditions. In contrast, the addition of oxygen to the anoxic sediments resulted in an approximately tenfold increase in methane oxidation relative to the anoxic incubations. Phylogenetic and isotopic evidence indicate that both Type I and Type II aerobic methanotrophs were growing on methane under both oxic and anoxic conditions, although methane assimilation rates were an order of magnitude higher under oxic conditions. While the anaerobic electron acceptor responsible for AOM could not be identified, these findings expand our understanding of the metabolic versatility of canonically aerobic methanotrophs under anoxic conditions, with important implications for future investigations to identify methane oxidation processes. Bacterial AOM by facultative aerobic methane oxidizers might be of much larger environmental significance in reducing methane emissions than previously thought.

scholarly journals Comparison of Aerobic Methanotrophic Communities in Littoral and Profundal Sediments of Lake Constance by a Molecular Approach

2007 ◽  
Vol 73 (13) ◽  
pp. 4389-4394 ◽  
Author(s):  
Monali Rahalkar ◽  
Bernhard Schink
Keyword(s):  
16S Rrna ◽  
Lake Constance ◽  
Gene Clone ◽  
Rrna Gene ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Molecular Approach ◽  
Clone Libraries ◽  
Methanotrophic Communities ◽  
Prominent Peak

ABSTRACT Analysis of pmoA and 16S rRNA gene clone libraries of methanotrophic bacteria in Lake Constance revealed an overall dominance of type I methanotrophs in both littoral and profundal sediments. The sediments exhibited minor differences in their methanotrophic community structures. Type X methanotrophs made up a significant part of the clone libraries only in the profundal sediment and were also found only there as a prominent peak by T-RFLP analyses.

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