Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Bissett, Andrew; Fitzgerald, Anna; Meintjes, Thys; Mele, Pauline M.; Reith, Frank; Dennis, Paul G.; Breed, Martin F.; Brown, Belinda; Brown, Mark V.; Brugger, Joël; Byrne, Margaret; Caddy‐Retalic, Stefan; Carmody, Bernie; Coates, David; Correa, Carolina; Ferrari, Belinda C.; Gupta, Vadakattu V. S. R.; Hamonts, Kelly; Haslem, Asha; Hugenholtz, Philip; Karan, Mirko; Koval, Jason C.; Lowe, Andrew J.; Macdonald, Stuart; McGrath, Leanne; Martín, David San; Morgan, Matt; North, Kristin I.; Paungfoo‐Lonhienne, Chanyarat; Pendall, Elise; Phillips, Lori A.; Pirzl, Rebecca; Powell, Jeff R.; Ragan, Mark A.; Schmidt, Susanne; Seymour, Nicole P.; Snape, Ian; Stephen, J.; Stevens, Matthew P.; Tinning, Matt; Williams, Kristen J.; Yeoh, Yun Kit; Zammit, Carla M.; Young, Andrew

doi:10.1186/s13742-016-0126-5

Cited by 207 publications

(248 citation statements)

References 47 publications

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“…The most abundant soil taxa were members of the Alphaproteobacteria , Actinobacteria, and Acidobacteria consistent with previous studies 25, 26 . Collectively, they represented 79.6% of taxa in each soil based on relative abundance (Supplementary Fig.…”

Section: Resultssupporting

confidence: 91%

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

et al. 2017

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Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angiosperms across a soil chronosequence using 16S rRNA gene amplicon profiling. We confirm that soil type is the primary determinant of root-associated bacterial community composition, but also observe a significant correlation with plant phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium, and Burkholderia, and major uncharacterized lineages such as WPS-2, Ellin329, and FW68. We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. This lends support to the inference that a core root microbiome has evolved with terrestrial plants over their 400 million year history.

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Section: Resultssupporting

confidence: 91%

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

et al. 2017

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“…Our study includes soil samples from 647 locations in the Southern Hemisphere, from Australia (541) to Antarctica (106), which were collected by the Biomes of Australia Soil Environments (BASE) project (Bissett et al 2016, Appendix S1: Fig. S1).…”

Section: Study Sitesmentioning

confidence: 99%

“…S1). Composite soil samples from nine discrete sites within the 25 9 25 m plots were collected from the top 0-0.1 m as described in Bissett et al (2016). Field information was collected between 2011 and 2014 from 25 9 25 m plots.…”

Section: Study Sitesmentioning

confidence: 99%

Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere

Delgado‐Baquerizo

Reith

Dennis

et al. 2018

Ecology

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The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.

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“…We determined the microbial community structure of the three soil samples from Robinson Ridge and three from Adams Flat. For both sites, the bacterial and archaeal community structure was determined by 16S rRNA gene amplicon sequencing as described previously 32,38 . Community alpha diversity was inferred from the amplicon sequencing data by calculating observed richness, Chao1, and the Shannon index (H′ ) as described 11 .…”

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confidence: 99%

Atmospheric trace gases support primary production in Antarctic desert surface soil

Greening

Vanwonterghem

et al. 2017

Nature

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307

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Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities 1-3 . Given that phototroph abundance varies across these Antarctic soils 2,4 , an enduring question is what supports life in those communities with low photosynthetic capacity 3,5 . Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation 6,7 . Soil microcosms aerobically scavenged atmospheric H 2 and CO at rates sufficient to sustain their theoretical maintenance energy and mediated substantial levels of chemosynthetic but not photosynthetic CO 2 fixation. We propose that atmospheric H 2 , CO 2 and CO provide dependable sources of energy and carbon to support these communities, which suggests that atmospheric energy sources can provide an alternative basis for ecosystem function to solar or geological energy sources 8,9 . Although more extensive sampling is required to verify whether this process is widespread in terrestrial Antarctica and other oligotrophic habitats, our results provide new understanding of the minimal nutritional requirements for life and open the possibility that atmospheric gases support life on other planets.Terrestrial Antarctica is among the most extreme environments on Earth. Its inhabitants experience the cumulative stresses of freezing temperatures, limited carbon, nitrogen and water availability, strong UV radiation, and frequent freeze-thaw cycles 2,10,11 . Although it was once believed that these conditions restrict life, we now know that the continent hosts a surprising diversity of macrofauna and microbiota 1,2,12 . Surveys indicate that the phylum-level composition of microbial communities in Antarctic soils is similar to those of temperate soils 3 , but Antarctic communities are highly specialized at the species level and strongly structured by physicochemical factors 1,3,10 . In many Antarctic soils, microorganisms are thought to live in dormant states 2 , with metabolic energy directed towards cell maintenance rather than growth 13 . However, it is unclear how these communities obtain the energy and carbon needed for maintenance, given that these soils are often low in organic carbon and contain few classical primary producers 2,5 .

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Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Cited by 207 publications

References 47 publications

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere

Atmospheric trace gases support primary production in Antarctic desert surface soil

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