Studying plant–microbe interactions using stable isotope technologies

Prosser, James I.; Rangel‐Castro, J. Ignacio; Killham, Ken

doi:10.1016/j.copbio.2006.01.001

Cited by 74 publications

(43 citation statements)

References 21 publications

(29 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The combination of 13 C stable isotope and PLFA analysis through Gas Chromatography-Combustion-Isotope Ratio Mass Spectrometry (GC-C-IRMS) has made it possible to trace the flow of C from a 13 C-labeled substrate into the PLFA fraction of the microbial communities (Boschker et al, 1998), and to identify the microbial communities actively assimilating the labeled substrate-derived C. This combined approach is unique as it allows to assess the specifically "active" proportion of the microbial community and to link biogeochemical processes with microbial identity. Stable isotope probing (SIP) of PLFA has been successfully attained through laboratory incubations with 13 C enriched substrate additions (Waldrop and Firestone, 2004), in situ enriched substrate additions (Williams et al, 2006), as well as in situ 13 CO 2 pulse labeling of growing plants (Treonis et al, 2004;Prosser et al, 2006;Denef et al, 2007;Lu et al, 2007). By using in situ PLFA-based SIP analysis, several studies have demonstrated a dominant contribution of fungi in the immediate assimilation of rhizosphere-derived C in grasslands (Butler et al, 2003;Treonis et al, 2004;Olsson and Johnson, 2005;Denef et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

Balasooriya

Denef

Peters

et al. 2008

Hydrol. Earth Syst. Sci.

View full text Add to dashboard Cite

Abstract. Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; Caricetum gracilis at the wet depression and Arrhenatheretum elatioris at the drier upper site. Microbial community structural changes were studied by a combined in situ 13 CO 2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of rootderived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.

show abstract

Section: Introductionmentioning

confidence: 99%

Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

Balasooriya

Denef

Peters

et al. 2008

Hydrol. Earth Syst. Sci.

View full text Add to dashboard Cite

show abstract

“…The recent development of stable isotope probing (SIP) (Radajewski et al, 2000) and its application to tracking plant-derived C into microbial nucleic acids (Rangel-Castro et al, 2005;Lu et al, 2006;Prosser et al, 2006;Neufeld et al, 2007) or other biochemical markers (Treonis et al, 2004;Paterson et al, 2007) provide the opportunity to understand the functional diversity of plant-associated bacterial communities.…”

Section: Introductionmentioning

confidence: 99%

Plant host habitat and root exudates shape soil bacterial community structure

et al. 2008

Self Cite

View full text Add to dashboard Cite

The rhizosphere is active and dynamic in which newly generated carbon, derived from root exudates, and ancient carbon, in soil organic matter (SOM), are available for microbial growth. Stable isotope probing (SIP) was used to determine bacterial communities assimilating each carbon source in the rhizosphere of four plant species. Wheat, maize, rape and barrel clover (Medicago truncatula) were grown separately in the same soil under 13 CO 2 (99% of atom 13 C) and DNA extracted from rhizosphere soil was fractionated by isopycnic centrifugation. Bacteria-assimilating root exudates were characterized by denaturing gradient gel electrophoresis (DGGE) analysis of 13 C-DNA and root DNA, whereas those assimilating SOM were identified from 12 C-DNA. Plant species root exudates significantly shaped rhizosphere bacterial community structure. Bacteria related to Sphingobacteriales and Myxococcus assimilated root exudates in colonizing roots of all four plants, whwereas bacteria related to Sphingomonadales utilized both carbon sources, and were identified in light, heavy and root compartment DNA. Sphingomonadales were specific to monocotyledons, whereas bacteria related to Enterobacter and Rhizobiales colonized all compartments of all four plants, used both fresh and ancient carbon and were considered as generalists. There was also evidence for an indirect important impact of root exudates, through stimulation of SOM assimilation by a diverse bacterial community.

show abstract

“…However, for ammonia oxidizers and other groups, there is little direct evidence about which strains within diverse communities are active under particular conditions or the extent of competition for substrates. Stable isotope probing (SIP) (24,27) of nucleic acids provides direct evidence of which members of mixed communities are active. This involves addition of substrates labeled with a stable isotope (most commonly 13 C), extraction of nucleic acids, separation of 12 C-and 13 C-labeled nucleic acids by density gradient centrifugation, and subsequent molecular analysis.…”

mentioning

confidence: 99%

Stable Isotope Probing Analysis of Interactions between Ammonia Oxidizers

Tourna

Freitag

Prosser

2010

Appl Environ Microbiol

View full text Add to dashboard Cite

The response of natural microbial communities to environmental change can be assessed by determining DNA-or RNA-targeted changes in relative abundance of 16S rRNA gene sequences by using fingerprinting techniques such as denaturing gradient gel electrophoresis (DNA-DGGE and RNA-DGGE, respectively) or by stable isotope probing (SIP) of 16S rRNA genes following incubation with a 13 C-labeled substrate (DNA-SIP-DGGE). The sensitivities of these three approaches were compared during batch growth of communities containing two or three Nitrosospira pure or enriched cultures with different tolerances to a high ammonia concentration. Cultures were supplied with low, intermediate, or high initial ammonia concentrations and with 13 C-labeled carbon dioxide. DNA-SIP-DGGE provided the most direct evidence for growth and was the most sensitive, with changes in DGGE profiles evident before changes in DNA-and RNA-DGGE profiles and before detectable increases in nitrite and nitrate production. RNA-DGGE provided intermediate sensitivity. In addition, the three molecular methods were used to follow growth of individual strains within communities. In general, changes in relative activities of individual strains within communities could be predicted from monoculture growth characteristics. Ammonia-tolerant Nitrosospira cluster 3b strains dominated mixed communities at all ammonia concentrations, and ammonia-sensitive strains were outcompeted at an intermediate ammonia concentration. However, coexistence of ammonia-tolerant and ammonia-sensitive strains occurred at the lowest ammonia concentration, and, under some conditions, strains inhibited at high ammonia in monoculture were active at high ammonia in mixed cultures, where they coexisted with ammonia-tolerant strains. The results therefore demonstrate the sensitivity of SIP for detection of activity of organisms with relatively low yield and low activity and its ability to follow changes in the structure of interacting microbial communities.

show abstract

Studying plant–microbe interactions using stable isotope technologies

Cited by 74 publications

References 21 publications

Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

Plant host habitat and root exudates shape soil bacterial community structure

Stable Isotope Probing Analysis of Interactions between Ammonia Oxidizers

Contact Info

Product

Resources

About