scholarly journals The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12176
Author(s):  
Micaela Schagen ◽  
Jason Bosch ◽  
Jenny Johnson ◽  
Robbert Duker ◽  
Pedro Lebre ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Complete Removal ◽  
Sequence Variant ◽  
Soil Bacterial Diversity ◽  
Starting Point ◽  
Soil Bacterial

This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.

scholarly journals Perennials but not slope aspect affect the diversity of soil bacterial communities in the northern Negev Desert, Israel

Soil Research ◽  
2018 ◽  
Vol 56 (2) ◽  
pp. 123 ◽  
Author(s):  
Ahuva Vonshak ◽  
Menachem Y. Sklarz ◽  
Ann M. Hirsch ◽  
Osnat Gillor
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Plant Litter ◽  
Negev Desert ◽  
Slope Aspect ◽  
Desert Shrubs ◽  
Soil Bacterial

Underneath the canopy of perennials in arid regions, moderate soil temperature and evaporation, as well as plant litter create islands of higher fertility in the low-productivity landscape, known as ‘resource islands’. The sparse distribution of these resource islands is mirrored by soil microbial communities, which mediate a large number of biogeochemical transformations underneath the plants. We explored the link between the bacterial community composition and two prevalent desert shrubs, Zygophyllum dumosum and Artemisia herba-alba, on northern- and southern-facing slopes in the northern highlands of the Negev Desert (Israel), at the end of a drought winter mild rainy season. We sequenced the bacterial community and analysed the physicochemical properties of the soil under the shrub canopies and from barren soil in replicate slopes. The soil bacterial diversity was independent of slope aspect, but differed according to shrub presence or type. Links between soil bacterial community composition and their associated desert shrubs were found, enabling us to link bacterial diversity with shrub type or barren soils. Our results suggest that plants and their associated bacterial communities are connected to survival and persistence under the harsh desert conditions.

scholarly journals Pavement Overrides the Effects of Tree Species on Soil Bacterial Communities

2021 ◽  
Vol 18 (4) ◽  
pp. 2168
Author(s):  
Yinhong Hu ◽  
Weiwei Yu ◽  
Bowen Cui ◽  
Yuanyuan Chen ◽  
Hua Zheng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Tree Species ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Soil Bacterial Community ◽  
Soil Bacterial Communities ◽  
Pine Stands ◽  
Soil Bacterial

Human disturbance and vegetation are known to affect soil microorganisms. However, the interacting effects of pavement and plant species on soil bacterial communities have received far less attention. In this study, we collected soil samples from pine (Pinus tabuliformis Carr.), ash (Fraxinus chinensis), and maple (Acer truncatum Bunge) stands that grew in impervious, pervious, and no pavement blocks to investigate the way pavement, tree species, and their interaction influence soil bacterial communities by modifying soil physicochemical properties. Soil bacterial community composition and diversity were evaluated by bacterial 16S amplicon sequencing. The results demonstrated that soil bacterial community composition and diversity did differ significantly across pavements, but not with tree species. The difference in soil bacterial community composition across pavements was greater in pine stands than ash and maple stands. Soil bacterial diversity and richness indices decreased beneath impervious pavement in pine stands, and only bacterial richness indices decreased markedly in ash stands, but neither showed a significant difference across pavements in maple stands. In addition, bacterial diversity did not differ dramatically between pervious pavement and no pavement soil. Taken together, these results suggest that pavement overwhelmed the effects of tree species on soil bacterial communities, and had a greater effect on soil bacterial communities in pine stands, followed by ash and maple stands. This study highlights the importance of anthropogenic disturbance, such as pavement, which affects soil microbial communities.

scholarly journals Effects of carbon nanotubes and derivatives of graphene oxide on soil bacterial diversity

2019 ◽  
Author(s):  
Christian Forstner ◽  
Thomas G. Orton ◽  
Peng Wang ◽  
Peter M. Kopittke ◽  
Paul G. Dennis
Keyword(s):  
Carbon Nanotubes ◽  
Graphene Oxide ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
High Concentration ◽  
Soil Bacterial Diversity ◽  
Functionalized Graphene Oxide ◽  
Soil Bacterial

AbstractCarbon nanotubes (CNTs), reduced graphene oxide (rGO) and ammonia-functionalized graphene oxide (aGO), are nanomaterials that possess varied and useful properties. However, following their use, their release into the environment is inevitable. While CNTs have been shown to influence soil bacterial diversity, albeit at very high concentration, the effects of rGO have only been examined using pure bacterial cultures, and those of aGO are unknown. Here, we investigated the effects of CNTs, rGO and aGO, at three time points (7, 14 and 30 days), and over a range of concentrations (1 ng, 1 µg and 1 mg kg dry soil-1), on soil bacterial diversity using 16S rRNA amplicon sequencing. Graphite was included to facilitate comparisons with a similar and naturally occurring carbon material, while the inclusion of GO allowed the effects of GO modification to be isolated. Bacterial community composition, but not alpha diversity, was altered by all treatments except the low GO, low rGO and high aGO treatments on day 14 only. In all cases, the nanomaterials led to shifts in community composition that were of similar magnitude to those induced by graphite and GO, albeit with differences in the taxa affected. Our study highlights that nanocarbon materials can induce changes in soil bacterial diversity, even at doses that are environmentally realistic.

scholarly journals Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

2021 ◽  
Vol 12 (1) ◽  
pp. 157-172
Author(s):  
Shankar G. Shanmugam ◽  
Normie W. Buehring ◽  
Jon D. Prevost ◽  
William L. Kingery
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Production System ◽  
Soil Microbial Community ◽  
Production Systems ◽  
Bacterial Community Composition ◽  
Soybean Production ◽  
Soil Microbial ◽  
Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

scholarly journals Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

2021 ◽  
Vol 11 (3) ◽  
pp. 918
Author(s):  
Lingzi Mo ◽  
Augusto Zanella ◽  
Xiaohua Chen ◽  
Bin Peng ◽  
Jiahui Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Soil Dna ◽  
Urban Green ◽  
Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

Impacts of invasive plant species on soil biodiversity: a case study of dog-strangling vine (Vincetoxicum rossicum) in a Canadian National Park

2018 ◽  
Vol 98 (4) ◽  
pp. 716-723 ◽  
Author(s):  
Laura N. Bugiel ◽  
Stuart W. Livingstone ◽  
Marney E. Isaac ◽  
Roberta R. Fulthorpe ◽  
Adam R. Martin
Keyword(s):  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Invasive Plant ◽  
Bacterial Community Composition ◽  
Anthropogenic Disturbances ◽  
Soil Parameters ◽  
Invasive Plant Species ◽  
Vincetoxicum Rossicum ◽  
Soil Bacterial

Soil microbial diversity is expected to be altered by the establishment of invasive plant species, such as dog-strangling vine (DSV) [Vincetoxicum rossicum (Apocynaceae)]. However, in urban ecosystems where DSV invasion is high, there is little research evaluating the impacts of DSV and other anthropogenic disturbances on microbial diversity. Our study was based in Rouge National Urban Park, Canada, where we used terminal restriction fragment length polymorphism data to evaluate (i) if DSV has a detectable impact on soil bacterial community composition and (ii) if these impacts occur independently of other anthropogenic change or soil characteristics. Variation in soil bacterial communities was greatly reduced in DSV-invaded sites vs. less-invaded sites. The degree of DSV invasion independently explained 23.8% of variation in bacterial community composition: a value similar to the explanatory power of proximity to roadways (which explained 22.6% of the variation in community composition), and considerably greater than soil parameters (pH, moisture, carbon, and nitrogen concentrations) which explained only between 6.0% and 10.0% of variation in bacterial community composition. Our findings indicate that DSV influences soil bacterial community composition independent of other anthropogenic disturbances and soil parameters, with potential impacts on multiple facets of plant–soil interactions and plant invasion dynamics.

scholarly journals Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mayank Krishna ◽  
Shruti Gupta ◽  
Manuel Delgado – Baquerizo ◽  
Elly Morriën ◽  
Satish Chandra Garkoti ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Bacterial Communities ◽  
Secondary Succession ◽  
Positive Association ◽  
Ecological Networks ◽  
Growth Stages ◽  
Ecosystem Recovery ◽  
Soil Bacterial

Abstract This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

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