Ammonia-Oxidizing Archaea Dominate Ammonia-Oxidizing Communities within Alkaline Cave Sediments

Zhao, Rui; Wang, Hongmei; Yang, Huan; Yun, Yuan; Barton, Hazel A.

doi:10.1080/01490451.2016.1225861

Cited by 18 publications

(30 citation statements)

References 83 publications

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“…Consequently, they contribute to the nutrient cycle of the cave. In parallel with the results of our study, AOA were found to be more dominant than ammonia oxidizing bacteria in Heshang Cave and Weebubbie Cave in China (Tetu et al 2013;Zhao et al 2017). It was suggested that the high level of AOA results from the high substrate affinity that allows them to multiply at lower ammonia concentrations than other organisms (Martens-Habbena et al 2009).…”

Section: Discussionsupporting

confidence: 88%

“…Their presence in caves has been widely identified in the sulfide rich environments (Macalady et al 2006;Jones et al 2012;Jones et al 2014;Gulecal-Pektas & Temel 2017). However, Thermoplasmata-related 16S rRNA sequences have been recently observed in all moonmilk (Reitschuler et al 2014;Reitschuler et al 2015) and cave sediments on a dry stream bed (Zhao et al 2017).…”

Section: Discussionmentioning

confidence: 99%

“…Only the phylum Thaumarchaeota and Euryarchaeota were identified in the Dupnisa Cave. The newly discovered Thaumarchaeota is known to be a chemoautotrophic ammonia oxidizer and is remarkable for its ability to developing in oligotrophic environments such as caves (Martens-Habbena et al 2009;Pester et al 2011;Ortiz et al 2014;Kimble 2017;Zhao et al 2017). In caves, ammonia from organic matter mineralization and / or guano deposits may be an energy source for chemolithotrophic organisms (Hathaway et al 2014).…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, Thaumarchaeota (over 80 %) was identified as the dominant archaeal phylum in the Dupnisa Cave, like in Kartchner Caverns (Arizona, USA) and Weebubbie Cave (Arizona, USA) (Bates et al 2011;Tetu et al 2013). Members of Thaumarchaeota are the dominant players in global nitrification (Stahl &De la Torre 2012;Ortiz et al 2014;Zhao et al 2017). They could be important since the nitrogen cycle provides nutrients and energy for microorganisms in oligotrophic environments such as caves (Tetu et al 2013;Ortiz et al 2014;Kimble 2017;Zhao et al 2017).…”

Section: Discussionmentioning

confidence: 99%

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The microbial community structure of the Dupnisa cave in Kırklareli, Turkey

Doğruöz-Güngör

2020

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Cave ecosystems count to be extreme environments due to their stable temperature, darkness, high humidity rates, and limited organic materials. In this context, these ecosystems represent invaluable laboratories for microbiological studies. Although there are common features between the microorganism groups obtained from the culture-based microbiological studies conducted in the caves and the groups highlighted through molecular methods, the microorganism groups determined through this last method are richer. The detected microorganisms are variable depending on the characteristics of each cave. The aim of this study is to determine the microbial diversity in samples taken from 5 different regions (including regions visited by tourists) of Dupnisa Cave and to reveal the differences between these regions. This is the first microbiological study running in cave sediments of Dupnisa Cave System situated in the north-western of Turkey. In this study, using the Illumina MiSeq next-generation sequencing approach for analyses of Dupnisa Cave samples, 14 phyla and 298 genera as well as 2 phyla and 20 genera can be attributed to bacterial and archaea OTUs, respectively. Moreover, the bacterial community is dominated by the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi and Acidobacteria distributed with 1 % and above. Archaeal community is represented by Thaumarchaeota and Euryarchaeota phyla. Proteobacteria is the most dominant bacterial phylum and Thaumarchaeota dominates the archaeal phyla. The highest number of types of bacteria according to Chao 1 richness estimation index were found at point AF (cave entrance / sediment), and that of types of archaea were found at point F2 (touristic area 2 / cave sediment). F2 was determined as the sampling point with the highest diversity of archaeal and bacterial genera according to Shannon-Wiener diversity index.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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The microbial community structure of the Dupnisa cave in Kırklareli, Turkey

Doğruöz-Güngör

2020

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“…Future research should compare results from pristine soils with those known to be impacted by acidification, as well as focus on diversity changes at higher taxonomic resolution. For instance, changes in pH and lower NH 3 in a soil environment (Xu and Gao, 2011) have been linked to shifts from ammonia-oxidizing bacteria to archaea (Zhao et al, 2016). Recently, soil acidification due to increasing acid rainfall in China was linked to a decrease in the microbial abundance (Wu et al, 2006; Xu et al, 2015), as well as the diversity (Zhalnina et al, 2015), which may result in a decrease in microbial functional diversity because functional gene diversity is significantly and positively correlated with taxonomic diversity (Fierer et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification

et al. 2016

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Enhanced monsoon duration and soil acidification from acid rain are expected to impact the distribution of microbial communities in surface and subsurface environments, although these impacts are poorly understood for most systems. In central China, soluble carbonate bedrock forms extensive karst landscapes. Current predictions are that the amount of monsoonal precipitation and acid rainfall in central China will increase, which is expected to lead to changes in the pH balance of karst ecosystems. To evaluate the role of pH, total organic carbon, and other geochemical parameters (e.g., Ca2+, Mg2+, NH4+, NOx, SO42-) in shaping bacterial communities within a single karst system in central China, samples were collected from the thin surface soils overlying Heshang Cave, cave sediments, and weathered cave passage rocks from the entrance, twilight, and dark zones, as well as from epikarstic drip waters inside the cave. Illumina sequencing of 16S rRNA genes and multivariate statistical analyses revealed that each tested community was distinct and the community variability was significantly correlated with pH, total organic carbon, and potassium concentrations. Specifically, surface soils were dominated by Acidobacteria, Verrucomicrobia and Planctomycetes, and diversity significantly decreased with acidic pH values. Nitrospirae, Gemmatimonadetes, Firmicutes, and Chloroflexi were unique to cave sediments, while Actinobacteria and Proteobacteria dominated weathered rocks and drip waters, respectively. The results reveal important implications regarding the effects of acidification on bacterial communities in karst areas, and on the control of pH in shaping bacterial communities throughout a karst system. Increased water flux into and through karst habitats due to monsoonal precipitation may result in deeper penetration of acidic solutions into karst and shift the bacterial communities inside the cave in the future.

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Major impacts of caving activities on cave microbial diversity: case study of Morca Cave, Turkey

Rachid

Güngör

2022

Int Microbiol

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Ammonia-Oxidizing Archaea Dominate Ammonia-Oxidizing Communities within Alkaline Cave Sediments

Cited by 18 publications

References 83 publications

The microbial community structure of the Dupnisa cave in Kırklareli, Turkey

The microbial community structure of the Dupnisa cave in Kırklareli, Turkey

The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification

Major impacts of caving activities on cave microbial diversity: case study of Morca Cave, Turkey

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