Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from <scp>S</scp>outh of <scp>C</scp>hile

Hernández, Marcela; Dumont, Marc G.; Calabi, Marcela; Basualto, Daniel; Conrad, Ralf

doi:10.1111/1758-2229.12109

Cited by 18 publications

(19 citation statements)

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“…Low abundance and low diversity of archaeal community, consisting almost exclusively of the specialized chemo‐litho‐autotrophic ammonia‐oxidizers Thaumarchaeota are quite surprising in this extreme environment. In acidic volcanic soils AOA were instead found to outnumber AOB and their abundance was proportional to the nitrification potential (Hernández et al ., ). The recently discovered ammonia‐oxidizing archaea (AOA) are widely distributed in other terrestrial geothermal systems (De la Torre et al ., ; Hatzenpichler et al ., ; Zhang et al ., ) and have an important role in the first and most limiting step of soil nitrification in both aquatic and terrestrial environments.…”

Section: Discussionmentioning

confidence: 99%

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites

et al. 2015

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This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils.

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Section: Discussionmentioning

confidence: 99%

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites

et al. 2015

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“…T‐RFLP was carried out as previously described with minor modification (Hernández et al ., ) to determine the composition of thaumarchaeotal amoA genes. Briefly, PCR was performed using the primers of CamoA‐19f/CamoA‐616r mentioned above, with FAM (6‐carboxyfluorescein) attached to the forward primer.…”

Section: Methodsmentioning

confidence: 99%

Ammonia oxidation-dependent growth of group I.1bThaumarchaeotain acidic red soil microcosms

Conrad

2014

FEMS Microbiol Ecol

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Accumulating evidence suggests that Thaumarchaeota may control nitrification in acidic soils. However, the composition of the thaumarchaeotal communities and their functioning is not well known. Therefore, we studied nitrification activity in relation to abundance and composition of Thaumarchaeota in an acidic red soil from China, using microcosms incubated with and without cellulose amendment. Cellulose was selected to simulate the input of crop residues used to increase soil fertility by local farming. Accumulation of NO3-(-N) was correlated with the growth of Thaumarchaeota as determined by qPCR of 16S rRNA and ammonia monooxygenase (amoA) genes. Both nitrification activity and thaumarchaeotal growth were inhibited by acetylene. They were also inhibited by cellulose amendment, possibly due to the depletion of ammonium by enhanced heterotrophic assimilation. These results indicated that growth of Thaumarchaeota was dependent on ammonia oxidation. The thaumarchaeotal 16S rRNA gene sequences in the red soil were dominated by a clade related to soil fosmid clone 29i4 within the group I.1b, which is widely distributed but so far uncultured. The archaeal amoA sequences were mainly related to the Nitrososphaera sister cluster. These observations suggest that fosmid clone 29i4 and Nitrososphaera sister cluster represent the same group of Thaumarchaeota and dominate ammonia oxidation in acidic red soil.

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“…Microbial communities associated with volcanoes have been studied in the lava flow soils, rocks, and/or glass found at Kilauea volcano, Hawaii (King 2003;Dunfield and King 2004;Nanba et al 2004;Gomez-Alvarez et al 2007;King and Weber 2008;Nacke et al 2011;King and King 2012); Mauna Loa, Hawaii (Crews et al 2001); Miyake Island, Japan (Ohta et al 2003); Llaima volcano, Chile (Hernandez et al 2014); and Mt. Hekla, Iceland (Kelly et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Pyrosequencing analysis of a bacterial community associated with lava‐formed soil from the Gotjawal forest in Jeju, Korea

Kim

Lee

Kim³

et al. 2015

MicrobiologyOpen

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In this study, we analyzed the bacterial diversity in soils collected from Gyorae Gotjawal forest, where globally unique topography, geology, and ecological features support a forest grown on basalt flows from 110,000 to 120,000 years ago and 40,000 to 50,000 years ago. The soils at the site are fertile, with rocky areas, and are home to endangered species of plants and animals. Rainwater penetrates to the groundwater aquifer, which is composed of 34% organic matter containing rare types of soil and no soil profile. We determined the bacterial community composition using 116,475 reads from a 454-pyrosequencing analysis. This dataset included 12,621 operational taxonomic units at 3% dissimilarity, distributed among the following groups: Proteobacteria (56.2%) with 45.7% of α-Proteobacteria, Actinobacteria (25%), Acidobacteria (10.9%), Chloroflexi (2.4%), and Bacteroidetes (0.9%). In addition, 16S rRNA gene sequences were amplified using polymerase chain reaction and domain-specific primers to construct a clone library based on 142 bacterial clones. These clones were affiliated with the following groups: Proteobacteria (56%) with 51% of α-Proteobacteria, Acidobacteria (7.8%), Actinobacteria (17.6%), Chloroflexi (2.1%), Bacilli (1.4%), Cyanobacteria (2.8%), and Planctomycetes (1.4%). Within the phylum Proteobacteria, 56 of 80 clones were tentatively identified as 12 unclassified genera. Several new genera and a new family were discovered within the Actinobacteria clones. Results from 454-pyrosequencing revealed that 57% and 34% of the sequences belonged to undescribed genera and families, respectively. The characteristics of Gotjawal soil, which are determined by lava morphology, vegetation, and groundwater penetration, might be reflected in the bacterial community composition.

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Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile

Cited by 18 publications

References 53 publications

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites

Ammonia oxidation-dependent growth of group I.1bThaumarchaeotain acidic red soil microcosms

Pyrosequencing analysis of a bacterial community associated with lava‐formed soil from the Gotjawal forest in Jeju, Korea

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