Novel group within the kingdom Crenarchaeota from boreal forest soil

108

This study determined nitrification activity and nitrifier community composition in soils under stands of red alder (Alnus rubra) and Douglas fir (Pseudotsuga menziesii) at two sites in Oregon. The H.J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon, has low net N mineralization and gross nitrification rates. Cascade Head Experimental Forest, in the Coast Range, has higher net N mineralization and nitrification rates and soil pH is lower. Communities of putative bacterial [ammonia-oxidizing bacteria (AOB)] and archaeal [ammonia-oxidizing archaea (AOA)] ammonia oxidizers were examined by targeting the gene amoA, which codes for subunit A of ammonia monooxygenase. Nitrification potential was significantly higher in red alder compared with Douglas-fir soil and greater at Cascade Head than H.J. Andrews. Ammonia-oxidizing bacteria amoA genes were amplified from all soils, but AOA amoA genes could only be amplified at Cascade Head. Gene copy numbers of AOB and AOA amoA were similar at Cascade Head regardless of tree type (2.3-6.0 x 10(6)amoA gene copies g(-1) of soil). DNA sequences of amoA revealed that AOB were members of Nitrosospira clusters 1, 2 and 4. Ammonia-oxidizing bacteria community composition, determined by terminal restriction fragment length polymorphism (T-RFLP) profiles, varied among sites and between tree types. Many of the AOA amoA sequences clustered with environmental clones previously obtained from soil; however, several sequences were more similar to clones previously recovered from marine and estuarine sediments. As with AOB, the AOA community composition differed between red alder and Douglas-fir soils.

Section: Discussionmentioning

confidence: 76%

Community composition of ammonia‐oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon

Boyle-Yarwood¹,

Bottomley

Myrold³

2008

108

“…Polymerase chain reaction products were obtained using primers Ar3F (Giovannoni et al, 1988) and Ar9R (Jurgens et al, 1997) (Table 1) generating a PCR product approximately 900 bp in length. For DGGE analysis, these PCR products were used as template in a nested PCR reaction using primers rSAf/PARCH519r (Table 1) generating a PCR product 118 bp in length (excluding primers).…”

Section: Nucleic Acid Extraction and Rt-pcr Amplification Of Archaealmentioning

confidence: 99%

“…Organisms belonging to the largely non-thermophilic 'Group 1' Crenarchaeota lineage appear to be ubiquitous in soil systems including grassland, forest, agricultural and rice field soils (e.g. Bintrim et al ., 1997;Jurgens et al ., 1997;Buckley et al ., 1998;Großkopf et al ., 1998;Nicol et al ., 2003a) and may be dominant over euryarchaeal populations in grassland soils (Nicol et al ., 2003b). Despite an increasing understanding of crenarchaeal diversity in the environment, little is known about the drivers of crenarchaeal diversity and their ecological functioning in soil systems (Nicol et al ., 2004).…”

Section: Introductionmentioning

confidence: 99%

Primary succession of soil Crenarchaeota across a receding glacier foreland

Nicol

Tscherko

Embley

et al. 2005

152

168

The development of soil archaeal community structures in relation to primary succession in bulk and rhizosphere soil was examined across the forefield of the receding Rotmoosferner glacier in Austria. Using cloning and denaturing gradient gel electrophoresis (DGGE) analysis of reverse transcription polymerase chain reaction (RT-PCR) products of extracted 16S rRNA, archaeal community structure was compared over a chronosequence representing approximately 150 years of soil development and to reference sites outside the glacier forefield, representing soil exposed for approximately 9500 years. Archaeal community composition was found to be dominated by members of the non-thermophilic or Group 1 Crenarchaeota, where a dramatic yet highly structured successional sequence was observed. Succession over the 150 years sequence could be identified as occurring in three stages, each of which had a phylogenetically distinct 1.1b crenarchaea community with those organisms present in pioneering and intermediate stages belonging to a lineage distinct from those in developed soils. Climax communities also contained organisms belonging to three other major non-thermophilic crenarchaeal lineages. Comparison of archaeal communities in the rhizosphere indicated that plant species composition was not the major driver of specific crenarchaeal populations. These results indicate the potential role of soil crenarchaea in the development of soil substrates, as well as ecological diversity within and between major Group 1 lineages.

“…Amplification 16S rRNA genes from Archaea for DGGE analysis using other general PCR primers (Ar3F, Ar9F; Jurgens et al, 1997) was also only successful with the 4.15 mbsf sediment. Therefore, nested PCR was applied Euryarchaeota Methane using marine sediment NANK-A-GW-56 Uncultured Archaea clone 33-FL49A00 (AF355958) 91 Crenarchaeota Mid-ocean ridge sediment a. Sequences named NANK-B-GW-nn are from the bands in Fig.…”

Section: Diversity Of Archaeamentioning

confidence: 99%

“…Primary amplification reactions for Bacteria were as described above. Amplification reaction mixtures for Ar3f, Ar9r were with primer pair 21F, 958R using PCR conditions as described in Jurgens et al (1997). Secondary PCR amplification (Bacteria 357F-GC, 518R, and Archaea SAf, PARCH 519R) were carried out without BSA in a 50 ml reaction mix (Webster et al, 2003).…”

Section: Pcr Reaction Conditionsmentioning

confidence: 99%

Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190

Newberry

Webster

Cragg

et al. 2004

183

172

Diversity of Bacteria and Archaea was studied in deep marine sediments by PCR amplification and sequence analysis of 16S rRNA and methyl co-enzyme M reductase (mcrA) genes. Samples analysed were from Ocean Drilling Program (ODP) Leg 190 deep subsurface sediments at three sites spanning the Nankai Trough in the Pacific Ocean off Shikoku Island, Japan. DNA was amplified, from three depths at site 1173 (4.15, 98.29 and 193.29 mbsf; metres below the sea floor), and phylogenetic analysis of clone libraries showed a wide variety of uncultured Bacteria and Archaea. Sequences of Bacteria were dominated by an uncultured and deeply branching 'deep sediment group' (53% of sequences). Archaeal 16S rRNA gene sequences were mainly within the uncultured clades of the Crenarchaeota. There was good agreement between sequences obtained independently by cloning and by denaturing gradient gel electrophoresis. These sequences were similar to others retrieved from marine sediment and other anoxic habitats, and so probably represent important indigenous bacteria. The mcrA gene analysis suggested limited methanogen diversity with only three gene clusters identified within the Methanosarcinales and Methanobacteriales. The cultivated members of the Methanobacteriales and some of the Methanosarcinales can use CO2 and H2 for methanogenesis. These substrates also gave the highest rates in 14C-radiotracer estimates of methanogenic activity, with rates comparable to those from other deep marine sediments. Thus, this research demonstrates the importance of the 'deep sediment group' of uncultured Bacteria and links limited diversity of methanogens to the dominance of CO2/H2 based methanogenesis in deep sub-seafloor sediments.