Dominant soil bacteria and their ecological attributes across the deserts in northern China

Wei Feng; Yuqing Zhang; Ru Yan; Zongrui Lai; Shugao Qin; Yanfei Sun; Weiwei She; Zhen Liu

doi:10.1111/ejss.12866

Globally Abundant “Candidatus Udaeobacter” Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging

mSphere ◽

10.1128/msphere.00186-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Inka M. Willms ◽

Anina Y. Rudolph ◽

Isabell Göschel ◽

Simon H. Bolz ◽

Dominik Schneider ◽

...

Keyword(s):

Multidrug Resistance ◽

Environmental Pollution ◽

Soil Bacteria ◽

Natural Habitat ◽

Genomic Analysis ◽

Trace Gas ◽

Dominant Soil ◽

Soil Ecosystems ◽

Terrestrial Habitats ◽

The Impact

ABSTRACT Verrucomicrobia affiliated with “Candidatus Udaeobacter” belong to the most abundant soil bacteria worldwide. Although the synthesis of antibiotics presumably evolved in soil, and environmental pollution with antimicrobials increases, the impact of these complex molecules on “Ca. Udaeobacter” remains to be elucidated. In this study, we demonstrate that “Ca. Udaeobacter” representatives residing in grassland as well as forest soil ecosystems show multidrug resistance and even take advantage of antibiotics release. Soils treated with up to six different antibiotics exhibited a higher “Ca. Udaeobacter” abundance than corresponding controls after 3, 8, and 20 days of incubation. In this context, we provide evidence that “Ca. Udaeobacter” representatives may utilize nutrients which are released due to antibiotic-driven lysis of other soil microbes and thereby reduce energetically expensive synthesis of required biomolecules. Moreover, genomic analysis revealed the presence of genes conferring resistance to multiple classes of antibiotics and indicated that “Ca. Udaeobacter” representatives most likely oxidize the trace gas H2 to generate energy. This energy might be required for long-term persistence in terrestrial habitats, as already suggested for other dominant soil bacteria. Our study illustrates, for the first time, that globally abundant “Ca. Udaeobacter” benefits from release of antibiotics, which confers advantages over other soil bacteria and represents a so-far overlooked fundamental lifestyle feature of this poorly characterized verrucomicrobial genus. Furthermore, our study suggests that “Ca. Udaeobacter” representatives can utilize H2 as an alternative electron donor. IMPORTANCE Soil bacteria have been investigated for more than a century, but one of the most dominant terrestrial groups on Earth, “Candidatus Udaeobacter,” remains elusive and largely unexplored. Its natural habitat is considered a major reservoir of antibiotics, which directly or indirectly impact phylogenetically diverse microorganisms. Here, we found that “Ca. Udaeobacter” representatives exhibit multidrug resistance and not only evade harmful effects of antimicrobials but even benefit from antibiotic pressure in soil. Therefore, “Ca. Udaeobacter” evidently affects the composition of soil resistomes worldwide and might represent a winner of rising environmental pollution with antimicrobials. In addition, our study indicates that “Ca. Udaeobacter” representatives utilize H2 and thereby contribute to global hydrogen cycling. The here-reported findings provide insights into elementary lifestyle features of “Ca. Udaeobacter,” potentially contributing to its successful global dissemination.

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The Influence of Vegetation Type on the Dominant Soil Bacteria, Archaea, and Fungi in a Low Arctic Tundra Landscape

Soil Science Society of America Journal ◽

10.2136/sssaj2011.0057 ◽

2011 ◽

Vol 75 (5) ◽

pp. 1756-1765 ◽

Cited By ~ 65

Author(s):

Haiyan Chu ◽

Josh D. Neufeld ◽

Virginia K. Walker ◽

Paul Grogan

Keyword(s):

Soil Bacteria ◽

Vegetation Type ◽

Arctic Tundra ◽

Dominant Soil ◽

Low Arctic

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Diversity of dominant soil bacteria increases with warming velocity at the global scale

10.1101/2020.04.27.063834 ◽

2020 ◽

Author(s):

Yoshiaki Kanzaki ◽

Kazuhiro Takemoto

Keyword(s):

Bacterial Diversity ◽

Soil Bacteria ◽

Environmental Changes ◽

Global Climate ◽

Aridity Index ◽

Global Scale ◽

Soil Bacterial Diversity ◽

Dominant Soil ◽

Global Soil ◽

Soil Bacterial

AbstractUnderstanding global soil bacterial diversity is important because of the key roles soil bacteria play in the global ecosystem. Given the effects of environmental changes (e.g., climate change and human effect) on the diversity of animals and plants, effects on soil bacterial diversity are expected; however, they have been poorly evaluated to date. Thus, in this study, we focused on the soil dominant bacteria because of their global importance and investigated the effects of warming velocity and human activities on their diversity. Using a global dataset of bacteria, we performed spatial analysis to evaluate the effects, while statistically controlling for the potential confounding effects of current climate and geographic parameters with global climate and geographic data. It was demonstrated that the diversity of the dominant soil bacteria was influenced globally by warming velocity (showing significant increases) in addition to aridity index (dryness) and pH. The effects of warming velocity were particularly significant in forests and grasslands. An effect from human activity was also observed, but it was secondary to warming velocity. These findings provide robust evidence, and advance our understanding of the effects of environmental changes (particularly global warming) on soil bacterial diversity at the global scale.

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Diversity of Dominant Soil Bacteria Increases with Warming Velocity at The Global Scale

Diversity ◽

10.3390/d13030120 ◽

2021 ◽

Vol 13 (3) ◽

pp. 120

Author(s):

Yoshiaki Kanzaki ◽

Kazuhiro Takemoto

Keyword(s):

Bacterial Diversity ◽

Human Activities ◽

Soil Bacteria ◽

Environmental Changes ◽

Global Climate ◽

Aridity Index ◽

Global Scale ◽

Soil Bacterial Diversity ◽

Dominant Soil ◽

Soil Bacterial

Understanding global soil bacterial diversity is important because of its role in maintaining a healthy global ecosystem. Given the effects of environmental changes (e.g., warming and human impact) on the diversity of animals and plants, effects on soil bacterial diversity are expected; however, they have been poorly evaluated at the global scale to date. Thus, in this study, we focused on the dominant soil bacteria, which are likely critical drivers of key soil processes worldwide, and investigated the effects of warming velocity and human activities on their diversity. Using a global dataset of bacteria, we performed spatial analysis to evaluate the effects of warming velocity and human activities, while statistically controlling for the potentially confounding effects of current climate and geographic parameters with global climate and geographic data. We demonstrated that the diversity of the dominant soil bacteria was influenced globally, not only by the aridity index (dryness) and pH but also by warming velocity from the Last Glacial Maximum (21,000 years ago) to the present, showing significant increases. The increase in bacterial diversity with warming velocity was particularly significant in forests and grasslands. An effect of human activity was also observed, but it was secondary to warming velocity. These findings provide robust evidence and advance our understanding of the effects of environmental changes (particularly global warming) on soil bacterial diversity at the global scale.

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