scholarly journals Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

2013 ◽  
Vol 79 (23) ◽  
pp. 7290-7297 ◽  
Author(s):  
Larisa Lee-Cruz ◽  
David P. Edwards ◽  
Binu M. Tripathi ◽  
Jonathan M. Adams
Keyword(s):  
Forest Soil ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Forest Conversion ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Β Diversity ◽  
Logged Forest ◽  
Soil Bacterial

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.

scholarly journals Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia

2019 ◽  
Vol 20 (3) ◽  
pp. 811-818
Author(s):  
MARINI WIJAYANTI ◽  
ARIS TRI WAHYUDI ◽  
MUNTI YUHANA ◽  
MARTIN ENGELHAUPT ◽  
ANJA MERYANDINI
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
Soil Ph ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Bacterial Phyla ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Community Shift ◽  
Soil Bacterial

Abstract. Wijayanti M, Wahyudi AT, Yuhana M, Engelhaupt M, Meryandini A. 2019. Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia. Biodiversitas 20: 811-818. Land use change from forest to oil palm plantation at Sumatra could decrease biodiversity, including bacterial diversity. The case of Bukit Dua Belas transformation from forest to oil palm plantation was gotten for measuring shift community of soil bacterial in both areas. The diversity of bacterial communities from rainforest and oil palm plantation topsoil in Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices. Phylogenetic approach was used to reveal the community shift of bacterial phyla and genera in both areas. Ecological approach was carried out by measuring soil pH, TC (total carbon), TN (total nitrogen), AP (available phosphorous), bacterial diversity with Shannon and Simpson indices, and bacterial richness with Chao1-ACE index and OTUs. Bacterial diversity and richness on lowland forest topsoil and oil palm plantation soil were not different, as soil pH, TC, and TN as substrate factors were not different significantly. The majority of sequences related to Acidobacteria (56.33%), Proteobacteria (27.43%), Actinobacteria (7.11%), and Cyanobacteria (5.55%) were from forest; whereas those related to Acidobacteria (50.11%), Proteobacteria (31.63%), Actinobacteria (7.58%), Chloroflexi (2.60%), and Gemmatimonadetes (2.71%) invented from oil palm plantation. Acidobacteria was the most dominant phyla in both habitats, because soil pH in both areas was acidic (3.77 - 4.80 pHH2O). The genera of alpha-proteobacteria dominated in genera phylotype of bacterial 16S rRNA phylogenetic revealed in both forest and oil palm plantation topsoil. The most genera in phylogenetic tree are Burkholderia from Beta-proteobacteria. The bacterial community shift occurred in forest transformation, even though the oil palm plantation showed more bacterial phyla and genera than the lowland rainforest.

scholarly journals Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Ana Novoa ◽  
Jan-Hendrik Keet ◽  
Yaiza Lechuga-Lago ◽  
Petr Pyšek ◽  
Johannes J Le Roux
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Coastal Dunes ◽  
Coastal Dune ◽  
Western Coast ◽  
Carpobrotus Edulis ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

ABSTRACT Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.

scholarly journals Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought

2012 ◽  
Vol 7 (2) ◽  
pp. 384-394 ◽  
Author(s):  
Nicholas J Bouskill ◽  
Hsiao Chien Lim ◽  
Sharon Borglin ◽  
Rohit Salve ◽  
Tana E Wood ◽  
...  
Keyword(s):  
Tropical Forest ◽  
Forest Soil ◽  
Bacterial Communities ◽  
Soil Bacterial Communities ◽  
Tropical Forest Soil ◽  
Soil Bacterial

Deforestation for oil palm: impact on microbially mediated methane and nitrous oxide emissions, and soil bacterial communities

2019 ◽  
Vol 56 (3) ◽  
pp. 287-298 ◽  
Author(s):  
Thomas Kaupper ◽  
Stefanie Hetz ◽  
Steffen Kolb ◽  
Sukhwan Yoon ◽  
Marcus A. Horn ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Nitrous Oxide Emissions ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Functional Profiling and Distribution of the Forest Soil Bacterial Communities Along the Soil Mycorrhizosphere Continuum

2013 ◽  
Vol 66 (2) ◽  
pp. 404-415 ◽  
Author(s):  
S. Uroz ◽  
P. E. Courty ◽  
J. C. Pierrat ◽  
M. Peter ◽  
M. Buée ◽  
...  
Keyword(s):  
Forest Soil ◽  
Bacterial Communities ◽  
Soil Bacterial Communities ◽  
Functional Profiling ◽  
Soil Bacterial

Effects of the invasive plant garlic mustard (Alliaria petiolata) on bacterial communities in a northern hardwood forest soil

2010 ◽  
Vol 56 (1) ◽  
pp. 81-86 ◽  
Author(s):  
David J. Burke ◽  
Charlotte R. Chan
Keyword(s):  
Forest Soil ◽  
Plant Species ◽  
Bacterial Communities ◽  
Invasive Plant ◽  
Native Plants ◽  
Soil Samples ◽  
Alliaria Petiolata ◽  
Garlic Mustard ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

We compared the effects of the invasive plant Alliaria petiolata (garlic mustard) and 2 native plants on soil bacterial communities in a mature mesophytic forest. Soil samples were collected from plant patches containing either Alliaria or the native plants Allium tricoccum (wild leek) and Gallium triflorum (bedstraw). Since Alliaria litter contains secondary compounds that have reported antimicrobial properties, soil was collected outside the root zone of the plants but within the plant patches such that the soil would have been influenced by the litter of the respective plant species but not by plant roots. DNA was extracted from the soil samples and used to amplify the 16S rRNA gene region using bacterial specific primers. Terminal restriction fragment length polymorphism (TRFLP) profiles of each bacterial community were used to examine differences in bacterial communities among the plant species and between August and April sampling. Bacterial richness, evenness, and diversity were not significantly affected by plant species. Non-metric multidimensional scaling (NMS) suggested that differences existed between August and April sampling, but that plant species litter exerted a much weaker effect on soil bacterial communities. Soil physiochemical conditions were significantly correlated with soil bacterial communities and may underlie the observed seasonal changes in bacterial communities.

scholarly journals High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12105
Author(s):  
Fangnan Xiao ◽  
Yuanyuan Li ◽  
Guifang Li ◽  
Yaling He ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Soil Bacteria ◽  
High Throughput Sequencing ◽  
Soil Bacterial Community ◽  
Tarim River ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
And Function

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

scholarly journals Potential effects of temperature levels on soil bacterial community structure

2021 ◽  
Vol 292 ◽  
pp. 01008
Author(s):  
Jing Fang ◽  
Shuli Wei ◽  
Gongfu Shi ◽  
Yuchen Cheng ◽  
Xiangqian Zhang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Soil Bacteria ◽  
Soil Microorganisms ◽  
Temperature Gradients ◽  
Control Treatment ◽  
Effect Of Temperature ◽  
Main Reaction ◽  
Soil Bacterial Communities ◽  
Infrared Temperature Measurement ◽  
Soil Bacterial

Soil microorganisms play a crucial role in the response to global warming in terrestrial ecosystems. Soils with higher microbial diversity have more ecological functions, higher resistance to environmental stress and higher crop production capacity. At present, the research on the effect of temperature change on soil microorganisms mostly adopts the methods of outdoor infrared temperature measurement or exchange and transplantation of soil with different temperature zones. Here, we investigate how temperature gradients potentially affect soil bacterial communities to change. For this reason, we used indoor precise temperature control treatment and combined high-throughput sequencing with bioinformatics to systematically analyze the diversity and species composition of soil bacteria under different temperature gradients, and to clarify the variation trend and interaction relationships of different species with temperature gradients. The results showed that temperature significantly affected the Alpha diversity of soil bacterial communities (P<0.05).Soil bacteria has different sensitivity and adaptability to temperature. In the range of 0-40℃, insensitive bacteria includes Proteobacteria, Gemmatimonadetes and Chloroflexi. Sensitive bacteria includes Sphingomonas, Ellin6055 and norank_f_67-14. The main reaction types of two bacteria showed four trends: ① Proteobacteria and Sphingomonas showed an “arch” variation; ② Gemmatimonadetes and Chloroflexi showed “inverted arch”. ③ Norank_f_67-14 showed an “inverted S type” change; ④ Ellin6055 shows a” parabolic ” shape. In different classification levels such as phylum and genus, the higher the classification level is, the higher degree it is weakened by temperature on, and the lower the classification level is, the stronger effect temperature has on it. In short, when temperature changes, soil bacteria can respond positively or negatively according to their ability to adapt to temperature, and accordingly form certain regular changes.

scholarly journals Soil Bacterial Communities and Diversity in Alpine Grasslands on the Tibetan Plateau Based on 16S rRNA Gene Sequencing

2021 ◽  
Vol 9 ◽  
Author(s):  
Hongmao Jiang ◽  
Youchao Chen ◽  
Yang Hu ◽  
Ziwei Wang ◽  
Xuyang Lu
Keyword(s):  
Tibetan Plateau ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Alpine Grassland ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Alpine Grasslands ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Grassland Types

The Tibetan Plateau, widely known as the world’s “Third Pole,” has gained extensive attention due to its susceptibility to climate change. Alpine grasslands are the dominant ecosystem on the Tibetan Plateau, albeit little is known about the microbial community and diversity among different alpine grassland types. Here, soil bacterial composition and diversity in the upper soils of five alpine grassland ecosystems, alpine meadow (AM), alpine steppe (AS), alpine meadow steppe (AMS), alpine desert (AD), and alpine desert steppe (ADS), were investigated based on the 16S rRNA gene sequencing technology. Actinobacteria (46.12%) and Proteobacteria (29.67%) were the two dominant soil bacteria at the phylum level in alpine grasslands. There were significant differences in the relative abundance at the genus level among the five different grassland types, especially for the Rubrobacter, Solirubrobacter, Pseudonocardia, Gaiella, Haliangium, and Geodermatophilus. Six alpha diversity indices were calculated based on the operational taxonomic units (OTUs), including Good’s coverage index, phylogenetic diversity (PD) whole tree index, Chao1 index, observed species index, Shannon index, and Simpson index. The Good’s coverage index value was around 0.97 for all the grassland types in the study area, meaning the soil bacteria samplings sequenced sufficiently. No statistically significant difference was shown in other diversity indices’ value, indicating the similar richness and evenness of soil bacteria in these alpine grasslands. The beta diversity, represented by Bray–Curtis dissimilarity and the non-metric multidimensional scaling (NMDS), showed that OTUs were clustered within alpine grasslands, indicating a clear separation of soil bacterial communities. In addition, soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), pH, and soil water content (SWC) were closely related to the variations in soil bacterial compositions. These results indicated that soil bacterial taxonomic compositions were similar, while soil bacterial community structures were different among the five alpine grassland types. The environmental conditions, including SOM, TN, TP, pH, and SWC, might influence the soil bacterial communities on the Tibetan Plateau.

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