Isoprene-Degrading Bacteria from Soils Associated with Tropical Economic Crops and Framework Forest Trees

Abstract

Isoprene, a volatile hydrocarbon emitted largely by plants, plays an important role in regulating the climate in diverse ways, such as reacting with free radicals in the atmosphere to produce greenhouse gases and pollutants. Isoprene is both deposited and formed in soil, where it can be consumed by some soil microbes, although much remains to be understood about isoprene consumption in tropical soils. In this study, isoprene-degrading bacteria from soils associated with tropical plants were investigated by cultivation and cultivation-independent approaches. Soil samples were taken from beneath selected framework forest trees and economic crops at different seasons, and isoprene degradation in soil microcosms was measured after 96 h of incubation. Isoprene losses were 4–31% and 15–52% in soils subjected to a lower (7.2 × 105 ppbv) and a higher (7.2 × 106 ppbv) concentration of isoprene, respectively. Sequencing of 16S rRNA genes revealed that bacterial communities in soil varied significantly across plant categories (framework trees versus economic crops) and the presence of isoprene, but not with isoprene concentration or season. Eight isoprene-degrading bacterial strains were isolated from the soils and, among these, four belong to the genera Ochrobactrum, Friedmanniella, Isoptericola and Cellulosimicrobium, which have not been previously shown to degrade isoprene.

Peering down the sink: A review of isoprene metabolism by bacteria

“…For example, members of the β‐proteobacteria, particularly Variovorax spp., were abundant in willow soil (Larke‐Mejía et al, 2019) and the phyllosphere of willow and poplar trees (Crombie et al, 2018; Gibson et al, 2021). Framework trees, pioneer species used to aid the regeneration of lost forests, and economic crops, such as oil palm and sugar cane were the sources of previously unknown isoprene‐degrading genera; Cellulosimicrobium , Friedmanniella , Isoptericola , Ochrobactrum (Uttarotai et al, 2021). Alcaligenes sp.…”

Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest

“…strain 13f was isolated from topsoil (3 cm from the surface) beneath wild Himalayan cherry trees (Prunus cerasoides D. Don) in a restored forest area (18 • 51 51" N 98 • 50 51" E) located in Doi Suthep-Pui National Park, Chiang Mai, Thailand. A one-gram portion of the soil sample was suspended in 9 mL of minimal medium (composition described by Uttarotai et al [34]) in a vial (125 cm 3 ) and tightly closed with PTFE/silicone septum. Isoprene from Sigma-Aldrich (St Louis, MO, USA) (7.2 × 10 5 ppbv) was injected into the bottle containing the soil sample (isoprene for injection was prepared according to the method described by Acuña Alvarez et al [13]).…”

“…strain bl28ba, a known isoprene degrader isolated by Murphy [38], was included as a positive control. A loopful of the bacterial culture, grown on minimal medium agar supplied with isoprene (as described in Section 2.1), was resuspended in 100 µL of minimal medium, and transferred to 9.9 mL of minimal medium without isoprene, minimal medium with isoprene, and glucose/yeast-extract broth [34], also with isoprene. The media were contained in 125 cm 3 vials (as above).…”

“…For each enrichment, isoprene was supplied at 7.2 × 10 5 ppbv and 7.2 × 10 6 ppbv (achieved by injecting 0.1 mL and 1 mL of headspace isoprene gas (prepared as described above) into the vials, respectively). Every three days, bacterial growth was determined by OD 600 , measured by using a Jenway 7300 spectrophotometer (Jenway, Stone, UK), and residual isoprene concentrations were measured by using a Unicam 610 gas chromatograph (Unicam, Lisbon, Portugal) with a flame ionisation detector (FID) and a 10% Apiezon L CW column, following the conditions described by Uttarotai et al [34].…”

“…The strain was associated with wild Himalayan cherry, one of the indigenous tree species that has been recommended as a framework species for forest restoration [33]. Many isoprene-degrading bacteria, including Ochrobactrum, Arthrobacter, Bacillus, Friedmanniella, Klebsiella, Isoptericola, and Cellulosimicrobium, had been found in this location [34]. Here, we investigated the metabolism of isoprene by this Alcaligenes strain through its genome characterisation.…”