Bacterial Functional Redundancy along a Soil Reclamation Gradient

Abstract

A strategy to measure bacterial functional redundancy was developed and tested with soils collected along a soil reclamation gradient by determining the richness and diversity of bacterial groups capable of in situ growth on selected carbon substrates. Soil cores were collected from four sites along a transect from the Jamari tin mine site in the Jamari National Forest, Rondonia, RO, Brazil: denuded mine spoil, soil from below the canopy of invading pioneer trees, revegetated soil under new growth on the forest edge, and the forest floor of an adjacent preserved forest. Bacterial population responses were analyzed by amending these soil samples with individual carbon substrates in the presence of bromodeoxyuridine (BrdU). BrdU-labeled DNA was then subjected to a 16S-23S rRNA intergenic analysis to depict the actively growing bacteria from each site. The number and diversity of bacterial groups responding to four carbon substrates (L-serine, L-threonine, sodium citrate, and ␣-lactose hydrate) increased along the reclamation-vegetation gradient such that the preserved forest soil samples contained the highest functional redundancy for each substrate. These data suggest that bacterial functional redundancy increases in relation to the regrowth of plant communities and may therefore represent an important aspect of the restoration of soil biological functionality to reclaimed mine spoils. They also suggest that bacterial functional redundancy may be a useful indicator of soil quality and ecosystem functioning.

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

“…We used BrdU to identify active bacteria (Urbach et al, 1999;Yin et al, 2000;Mou et al, 2008). BrdU is incorporated into newly synthesised DNA upon replication and BrdU-labelled DNA can then be isolated by immunocapture (Urbach et al, 1999;Yin et al, 2000).…”

“…To circumvent this bottleneck, we exposed microorganisms to the thymidine analogue bromodeoxyuridine (BrdU) and sequenced the BrdUlabelled DNA after immunocapturing (Yin et al, 2000); this allowed us to identify metabolically active microorganisms upon amendment with model autochthonous and allochthonous DOC, respectively (Mou et al, 2008). Extracts were amended to benthic biofilms grown in situ above, around and below the treeline in three alpine catchments, allowing us to study diversity patterns of metabolically active biofilm communities and to relate these patterns to resource specialisation.…”

Bacterial community structure corresponds to performance during cathodic nitrate reduction

“…Relationships between bacterial diversity and system function are beginning to be examined for bacterial communities (Yin et al, 2000, Bell et al, 2005, Wittebolle et al, 2009). In our reactors, the active bacterial taxa richness was positively correlated (Po0.05) with current production.…”

Linking soil bacterial diversity to ecosystem multifunctionality using backward-elimination boosted trees analysis

“…For example, bacteria are thought to be flexible in resource requirements and physiological abilities (Prosser et al 2007) and to obtain new traits easily through horizontal gene transfers that are necessary for survival in a given habitat (Choi and Kim 2007;Thomas and Nielsen 2005). The high degree of ecological redundancy of bacteria can be inferred based on the unique aspects of the bacterial biology (Yin et al 2000). Then, if bacteria exhibit a high degree of ecological redundancy, the concept that more ecosystem functions require more species to sustain would not be expected.…”