Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China

Abstract

Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.

Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China

“…Considering group 1.1b of Thaumarchaeota was taxonomically classified as Nitrososphaera (Bomberg, 2016), the relative abundance of Nitrososphaera (group 1.1b) in this study was comparable to the data observed in our former study of the AOA, in which the Nitrososphaera cluster and the Nitrososphaera sister cluster together comprised 89.34% of the AOA sequences across the same soil samples (Liu et al, 2018). Thus, we hypothesized that the majority of archaea in black soils contribute to nitrification.…”

“…The copy number of the archaeal genes was calculated by a regression equation to convert the cycle threshold value to the known copy numbers in the standard curves. The copy numbers of the archaeal genes were converted into per gram of dry soil as described in our previous study (Liu et al, 2018). In addition, the ratio of between the archaeal and bacterial 16S rRNA gene copies was also calculated using abundance data of bacterial 16S rRNA genes reported previously (Liu et al, 2016a).…”

“…Our previous studies revealed the biogeographic distribution patterns of the bacterial and fungal communities (Liu et al, 2014, 2015), as well as the ammonia-oxidizing bacteria (AOB) and archaea (AOA) across the black soil zone in northeast China (Liu et al, 2018). We found that both the bacterial and fungal communities showed distinct geographic distribution in this region, and the soil pH and carbon content are two overarching edaphic factors that determine the distribution of the bacterial and fungal communities, respectively (Liu et al, 2014, 2015).…”

“…We found that both the bacterial and fungal communities showed distinct geographic distribution in this region, and the soil pH and carbon content are two overarching edaphic factors that determine the distribution of the bacterial and fungal communities, respectively (Liu et al, 2014, 2015). For ammonia oxidizers, we detected that the AOA showed more distinct biogeographic distribution patterns than the AOB across the black soil zone, and the soil pH was the predominant soil factor in shaping both the AOA and AOB community structures (Liu et al, 2018). However, the compositional and biogeographic distribution patterns of the archaea in this region have not been addressed.…”

The Biogeographical Distribution of Soil Bacterial Communities in the Loess Plateau as Revealed by High-Throughput Sequencing

“…Soil microorganisms from terrestrial habitats are key drivers of critical ecosystem services, such as nutrients cycling (Madsen, 2005 ), soil organic matter (SOM) stabilization and C sequestration (Grandy and Neff, 2008 ; Plaza et al, 2013 ). Although, recent investigations (Xiong et al, 2012 ; Liu et al, 2015 , 2018 ; Xia et al, 2016 ) across different ecosystems have exhibited distinct biogeographic distribution pattern of soil microbes, deeper insights into their distribution and relationship between microbial-mediated nutrient cycling is required to facilitate our understanding of such processes. In recent decades, developments in next-generation high-throughput sequencing have made comprehensive study of soil microbial communities affordable at various scales (Kuang et al, 2013 ; Wu et al, 2013 ; Liu J. et al, 2014 ; Zhang et al, 2018 ).…”