Forest soil bacteria able to produce homo and copolymers of polyhydroxyalkanoates from several pure and waste carbon sources

ABSTRACTTropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

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A COMMENT ON THE NUTRITIONAL GROUPING OF SOIL BACTERIA

Canadian Journal of Microbiology ◽

10.1139/m67-072 ◽

1967 ◽

Vol 13 (5) ◽

pp. 565-568 ◽

Cited By ~ 1

Author(s):

Veronica Sundman ◽

Gunnel Calberg

Keyword(s):

Carbon Source ◽

Forest Soil ◽

Soil Bacteria ◽

Mineral Nitrogen ◽

Bacterial Isolates

Bacterial isolates (512), mostly from forest soil, were studied by nutritional grouping methods. When glucose (the customary carbon source) was augmented with lactate, glycerol, acetate, and citrate, about 17% more organisms were able to develop in media containing mineral nitrogen.

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A dynamic rhizosphere interplay between tree roots and soil bacteria under drought stress

10.5194/egusphere-egu21-8069 ◽

2021 ◽

Author(s):

Yaarao Oppenheimer-Shaanan ◽

Gilad Jakoby ◽

Maya Laurenci Starr ◽

Romiel Karliner ◽

Gal Eilon ◽

...

Keyword(s):

Forest Soil ◽

Soil Bacteria ◽

Bacterial Species ◽

Root Exudation ◽

Nitrogen Sources ◽

Microbial Interactions ◽

Tree Roots ◽

Carbon And Nitrogen ◽

Custom Made ◽

Exudation Rate

Root exudates are thought to play an important role in plant-microbial interactions. In return, soil bacteria can increase the bioavailability of soil minerals, which is typically decreasing in situations such as drought. Here we describe an exudate-driven microbial priming on Cupressus saplings grown outside in forest soil in custom-made rhizotron boxes. A 1-month imposed drought and inoculations with Bacillus subtilis and Pseudomonas stutzeri, bacteria species forest soil isolation, were applied in a factorial design. We revealed that both bacteria associated with Cupressus roots and were more abundant in rhizosphere than in bulk soil. Moreover, root exudation rate increased in inoculated trees under drought with >100 first identified metabolites from Cupressus roots. Among these metabolites, phenolic acid compounds, quinate, and others, were used as carbon and nitrogen sources by both bacterial species. Furthermore, soil phosphorous bioavailability was maintained only in inoculated trees, where a drought-induced decrease in leaf phosphorus and iron was prevented. We provide evidence that changes in exudation rate and composition under drought and bacteria inoculation, support the idea of root recruitment of beneficial bacteria. In turn, trees secreted further carbon source to the rhizosphere and hosted more bacteria, benefited from improved nutrition.

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Asticcacaulis solisilvae sp. nov., isolated from forest soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.047423-0 ◽

2013 ◽

Vol 63 (Pt_10) ◽

pp. 3829-3834 ◽

Cited By ~ 14

Author(s):

Seil Kim ◽

Gyeongtaek Gong ◽

Tai Hyun Park ◽

Youngsoon Um

Keyword(s):

Forest Soil ◽

Dna Hybridization ◽

Type Species ◽

Sequence Similarity ◽

Carbon Sources ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Soil Isolate ◽

Prosthecate Bacterium

An obligately aerobic, chemoheterotrophic, mesophilic prosthecate bacterium, designated strain CGM1-3ENT, was isolated from the enrichment cultures of forest soil from Cheonggyesan Mountain, Republic of Korea. Cells were Gram-reaction-negative, motile rods (1.3–2.4 µm long by 0.30–0.75 µm wide) with single flagella. The strain grew at 10–37 °C (optimum 25–30 °C) and at pH 4.5–9.5 (optimum 5.0–7.0). The major cellular fatty acids were C16 : 0, C18 : 1ω7c 11-methyl, C12 : 1 3-OH and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c). The genomic DNA G+C content of strain CGM1-3ENT was 63.7 mol%. The closest phylogenetic neighbour to strain CGM1-3ENT was identified as Asticcacaulis biprosthecium DSM 4723T (97.2 % 16S rRNA gene sequence similarity) and the DNA–DNA hybridization value between strain CGM1-3ENT and A. biprosthecium DSM 4723T was less than 24.5 %. Strain CGM1-3ENT used d-glucose, d-fructose, sucrose, maltose, trehalose, d-mannose, d-mannitol, d-sorbitol, d-galactose, cellobiose, lactose, raffinose, fumarate, pyruvate, dl-alanine and glycerol as carbon sources. Based on data from the present polyphasic study, the forest soil isolate CGM1-3ENT is considered to represent a novel species of the genus Asticcacaulis , for which the name Asticcacaulis solisilvae sp. nov. is proposed. The type strain is CGM1-3ENT ( = AIM0088T = KCTC 32102T = JCM 18544T).

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Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems

Scientific Reports ◽

10.1038/srep25279 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 136

Author(s):

Rubén López-Mondéjar ◽

Daniela Zühlke ◽

Dörte Becher ◽

Katharina Riedel ◽

Petr Baldrian

Keyword(s):

Forest Soil ◽

Soil Bacteria ◽

Enzymatic Systems

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Purification and characterization of a GH43 β-xylosidase from Enterobacter sp. identified and cloned from forest soil bacteria

Microbiological Research ◽

10.1016/j.micres.2013.06.004 ◽

2014 ◽

Vol 169 (2-3) ◽

pp. 213-220 ◽

Cited By ~ 19

Author(s):

Eleonora Campos ◽

María José Negro Alvarez ◽

Gonzalo Sabarís di Lorenzo ◽

Sergio Gonzalez ◽

Marcela Rorig ◽

...

Keyword(s):

Forest Soil ◽

Soil Bacteria ◽

Purification And Characterization

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Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress

Annals of Microbiology ◽

10.1007/s13213-014-1002-0 ◽

2014 ◽

Vol 65 (3) ◽

pp. 1627-1637 ◽

Cited By ~ 49

Author(s):

Marcin Chodak ◽

Marcin Gołębiewski ◽

Justyna Morawska-Płoskonka ◽

Katarzyna Kuduk ◽

Maria Niklińska

Keyword(s):

Forest Soil ◽

Soil Bacteria ◽

Chemical Properties ◽

Soil Chemical Properties

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A dynamic rhizosphere interplay between tree roots and soil bacteria under drought

10.1101/2021.08.24.457490 ◽

2021 ◽

Author(s):

Yaara Oppenheimer-Shaanan ◽

Gilad Jakoby ◽

Maya Starr ◽

Romiel Karliner ◽

Gal Eilon ◽

...

Keyword(s):

Forest Soil ◽

Root Exudates ◽

Soil Bacteria ◽

Bacterial Species ◽

Root Exudation ◽

Pseudomonas Stutzeri ◽

Nitrogen Sources ◽

Microbial Interactions ◽

Tree Roots ◽

Custom Made

Root exudates are thought to play an important role in plant-microbial interactions. In return for nutrition, soil bacteria can increase the bioavailability of soil minerals. However, root exudates typically decrease in situations such as drought, calling into question the efficacy of bacteria-dependent mineral uptake in such stress. Here we tested the hypothesis of exudate-driven microbial priming on Cupressus saplings grown in forest soil in custom-made rhizotron boxes. A 1-month imposed drought and concomitant inoculations with Bacillus subtilis and Pseudomonas stutzeri, bacteria species isolated from the forest soil, were applied using factorial design. Direct bacteria counts and visualization by confocal microscopy showed that both bacteria associated with Cupressus roots. Interestingly, root exudation rates increased with bacteria under drought. Forty four metabolites in exudates were significantly different in concentration between irrigated and drought trees, including phenolic acid compounds and quinate, that were shown to be used as carbon and nitrogen sources by both bacterial species. Importantly, soil phosphorous bioavailability was maintained only in inoculated trees, mitigating drought-induced decrease in leaf phosphorus and iron. Our observations of increased root exudation rate when drought and inoculation regimes were combined, support the idea of root recruitment of beneficial bacteria.

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Fungal Taxa Target Different Carbon Sources in Forest Soil

Ecosystems ◽

10.1007/s10021-008-9186-4 ◽

2008 ◽

Vol 11 (7) ◽

pp. 1157-1167 ◽

Cited By ~ 130

Author(s):

China A. Hanson ◽

Steven D. Allison ◽

Mark A. Bradford ◽

Matthew D. Wallenstein ◽

Kathleen K. Treseder

Keyword(s):

Forest Soil ◽

Carbon Sources

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