Geospatial variation in co‐occurrence networks of nitrifying microbial guilds

Abstract

Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.

Diversifying Anaerobic Respiration Strategies to Compete in the Rhizosphere

“…Their availability in the rhizosphere is variable and depends on different biotic and abiotic factors. The bioavailability of N forms in soils, such as nitrate (NO − 3 ) and nitrite (NO − 2 ) is a dynamic balance influenced by microbial nitrification and denitrification (Jones and Hallin, 2018). NO − 2 formation occurs near the surface and NO − 2 concentration decrease rapidly with deep (Arth and Frenzel, 2000).…”

Comparison and Interpretation of Characteristics of Rhizosphere Microbial Communities in Three Blueberry Varieties: The Benefits to Blueberry Production

“…The correlations among OTUs of the rhizosphere microbial community of blueberry were calculated by using the SparCC algorithm (https://github.com/hallamlab/utilities/wiki/SparCC), which limits the number of spurious correlation identi ed (45,46). The threshold of absolute correlations among OTUs was set at 0.8 and the signi cant correlations with p value < 0.05 were visualized in Cytoscape (47) (version 3.7.1).…”

Comparison and Interpretation of Characteristics of Rhizosphere Microbiomes of Three Blueberry Varieties

“…The correlations among OTUs of the rhizosphere microbial community of blueberry were calculated by using the SparCC algorithm (https://github.com/hallamlab/utilities/wiki/SparCC), which limits the number of spurious correlation identi ed [47,48]. The threshold of absolute correlations among OTUs was set at 0.8 and the signi cant correlations with p value < 0.05 were visualized in Cytoscape [49] (version 3.7.1).…”