Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments

Authored by Hualong Wang^1,2, Raven Bier^3†, Laura Zgleszewski³, Marc Peipoch³, Emmanuel Omondi^4†, Atanu Mukherjee^4†, Feng Chen², Chuanlun Zhang^5,6,7 and Jinjun Kan^3,6,8*

Abstract

In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.

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1: College of Marine Life Sciences, Ocean University of China, Qingdao, China
2: Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
3: Microbiology Division, Stroud Water Research Center, Avondale, PA, United States
4: Rodale Institute, Kutztown, PA, United States
5: Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
6: Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
7: Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
8: Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China