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Purpose <p>Comammox <i>Nitrospira</i> (CMX), the sole known complete ammonia-oxidizing bacteria, have redefined the biogeochemical landscape of nitrification by mediating the full oxidation of ammonia to nitrate within a single organism. However, the regional-scale biogeographic patterns, community assembly dynamics, and environmental adaptation strategies of CMX across distinct terrestrial ecosystems remain elusive.</p> Materials and methods <p>We integrated high-throughput sequencing, co-occurrence network analysis, and null model approaches to investigate CMX communities in three distinct terrestrial ecosystem types.</p> Results and discussion <p>Results revealed striking ecosystem-specific differentiation in CMX community traits: rice and forest habitats have the higher alpha diversity (Shannon-Wiener, Simpson and Pielou’s evenness), while maize soils show the lowest diversity; conversely, the Chao 1 index is lowest in forest, and higher in maize and rice. CMX Clade A.2 dominated maize soils (93%), Clade B was most abundant in forest soils (51%), and rice soils harbored a relatively higher proportions of Clade A.2 (51%) and Clade A.3 (31%). Beta diversity analysis shows distinct separation of CMX communities across maize, rice, and forest ecosystems, while Constrained analysis of principal coordinates and Mantel tests revealed that latitude, mean annual temperature (MAT), and nitrate-nitrogen were the primary drivers shaping CMX community structure in maize ecosystems, latitude and mean annual precipitation (MAP) were the key environmental factors in rice ecosystems, whereas total carbon (TC) and C/N ratio predominantly governed community structure in forest ecosystems. Rice ecosystems exhibited a well-connected CMX co-occurrence pattern, followed by maize and forest ecosystems. Stochastic processes, particularly ecological drift and dispersal limitation, dominated CMX community assembly across all ecosystems, collectively contributing 66% (maize), 84% (rice), and 93% (forest) of the total assembly processes. Deterministic processes showed ecosystem-specific contributions, with homogeneous selection being most prominent in maize soils (33%). Niche breadth analysis demonstrated that CMX in maize soils exhibited the widest environmental adaptability, followed by rice and forest soils.</p> Conclusions <p>These ecosystem-specific differences in CMX community traits and assembly mechanisms reflect the ecological adaptation of CMX to distinct environmental conditions shaped by different land-use types. This work provides mechanistic insights into the biogeographic patterns of CMX communities and their implications for N cycling under global land-use change.</p>

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Community traits and assembly mechanisms of comammox Nitrospira across maize, rice, and forest ecosystems in Eastern China

  • 期刊论文

  • 发表日期：

    2026年6月18日

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  • Xiang Li,
  • Mingmei Lu,
  • Yarui Shi,
  • Tengyu Feng,
  • Xiaoting Zheng,
  • Ping Liu,
  • Ruixian Yang,
  • Kesheng Zhang,
  • Xuesong Luo

摘要

Purpose

Comammox Nitrospira (CMX), the sole known complete ammonia-oxidizing bacteria, have redefined the biogeochemical landscape of nitrification by mediating the full oxidation of ammonia to nitrate within a single organism. However, the regional-scale biogeographic patterns, community assembly dynamics, and environmental adaptation strategies of CMX across distinct terrestrial ecosystems remain elusive.

Materials and methods

We integrated high-throughput sequencing, co-occurrence network analysis, and null model approaches to investigate CMX communities in three distinct terrestrial ecosystem types.

Results and discussion

Results revealed striking ecosystem-specific differentiation in CMX community traits: rice and forest habitats have the higher alpha diversity (Shannon-Wiener, Simpson and Pielou’s evenness), while maize soils show the lowest diversity; conversely, the Chao 1 index is lowest in forest, and higher in maize and rice. CMX Clade A.2 dominated maize soils (93%), Clade B was most abundant in forest soils (51%), and rice soils harbored a relatively higher proportions of Clade A.2 (51%) and Clade A.3 (31%). Beta diversity analysis shows distinct separation of CMX communities across maize, rice, and forest ecosystems, while Constrained analysis of principal coordinates and Mantel tests revealed that latitude, mean annual temperature (MAT), and nitrate-nitrogen were the primary drivers shaping CMX community structure in maize ecosystems, latitude and mean annual precipitation (MAP) were the key environmental factors in rice ecosystems, whereas total carbon (TC) and C/N ratio predominantly governed community structure in forest ecosystems. Rice ecosystems exhibited a well-connected CMX co-occurrence pattern, followed by maize and forest ecosystems. Stochastic processes, particularly ecological drift and dispersal limitation, dominated CMX community assembly across all ecosystems, collectively contributing 66% (maize), 84% (rice), and 93% (forest) of the total assembly processes. Deterministic processes showed ecosystem-specific contributions, with homogeneous selection being most prominent in maize soils (33%). Niche breadth analysis demonstrated that CMX in maize soils exhibited the widest environmental adaptability, followed by rice and forest soils.

Conclusions

These ecosystem-specific differences in CMX community traits and assembly mechanisms reflect the ecological adaptation of CMX to distinct environmental conditions shaped by different land-use types. This work provides mechanistic insights into the biogeographic patterns of CMX communities and their implications for N cycling under global land-use change.