Abundance and community composition of free-living nematodes as a function of soil structure under different vineyard managements

2022 ◽  
Vol 170 ◽  
pp. 104291
Author(s):  
Steffen Schlüter ◽  
Eshel Gil ◽  
Tirza Doniger ◽  
Itaii Applebaum ◽  
Yosef Steinberger
2021 ◽  
Vol 9 (2) ◽  
pp. 171
Author(s):  
Bum Soo Park ◽  
Won-Ji Choi ◽  
Ruoyu Guo ◽  
Hansol Kim ◽  
Jang-Seu Ki

Bacteria are remarkably associated with the growth of green algae Tetraselmis which are used as a feed source in aquaculture, but Tetraselmis-associated bacterial community is characterized insufficiently. Here, as a first step towards characterization of the associated bacteria, we investigated the community composition of free-living (FLB) and particle-associated (PAB) bacteria in each growth phase (lag, exponential, stationary, and death) of Tetraselmis suecica P039 culture using pyrosequencing. The percentage of shared operational taxonomic units (OTUs) between FLB and PAB communities was substantially high (≥92.4%), but their bacterial community compositions were significantly (p = 0.05) different from each other. The PAB community was more variable than the FLB community depending on the growth phase of T. suecica. In the PAB community, the proportions of Marinobacter and Flavobacteriaceae were considerably varied in accordance with the cell number of T. suecica, but there was no clear variation in the FLB community composition. This suggests that the PAB community may have a stronger association with the algal growth than the FLB community. Interestingly, irrespective of the growth phase, Roseobacter clade and genus Muricauda were predominant in both FLB and PAB communities, indicating that bacterial communities in T. suecica culture may positively affect the algae growth and that they are potentially capable of enhancing the T. suecica growth.


2017 ◽  
Vol 93 (6) ◽  
Author(s):  
Dayong Zhao ◽  
Huimin Xu ◽  
Jin Zeng ◽  
Xinyi Cao ◽  
Rui Huang ◽  
...  

2014 ◽  
Vol 81 (4) ◽  
pp. 1463-1471 ◽  
Author(s):  
Stefan Thiele ◽  
Bernhard M. Fuchs ◽  
Rudolf Amann ◽  
Morten H. Iversen

ABSTRACTDue to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washedin situto prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescencein situhybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather thande novocolonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.


2020 ◽  
Author(s):  
Jeroen Zethof ◽  
Antje Bettermann ◽  
Cordula Vogel ◽  
Doreen Babin ◽  
Erik Cammeraat ◽  
...  

<p>Individual plant species form so-called resource islands in the barren semiarid landscape, whereby many soil properties are enhanced including soil structure. Within the soil structure, mostly studied as soil aggregates, microaggregates (<250µm) form fundamental components, reducing potential erosion of finer particles and subsequent loss of nutrients. Extracellular polymeric substances (EPS) are considered an important glue determining aggregation in addition to inorganic binding agents such as carbonates and clay minerals. However, the role of the soil prokaryotic community in EPS formation and consequently for microaggregation in natural environments has not been clarified yet. EPS should be particularly important under semiarid conditions as they form a protection mechanism of the prokaryotes against desiccation. Therefore, we examined the influence of the prokaryotic community on soil EPS content and subsequently on soil aggregation in semiarid grasslands, with respect to the parent material of soil formation, common plant species and the distance to the plant.</p><p>During two sampling campaigns in spring 2017 and 2018, soil samples were taken over a distance gradient from two major semiarid grassland plant species in Southern Spain, the legume shrub <em>Anthyllis cytisoides</em> and the grass tussock <em>Macrochloa tenacissima</em>, to the surrounding bare soil. While topsoil was sampled in five distances to the plant during the first sampling campaign, the second one focused stronger on the root influence, hence rhizoplane and rhizosphere were sampled. Additionally, two sites with different parent materials were chosen to scale the effect of EPS on soil aggregation in the presence of inorganic binding agents (here carbonates). Total community DNA and EPS were extracted, followed by quantification of EPS-saccharides and bacterial abundance, as well as examination of the prokaryotic community composition by Illumina amplicon sequencing of the 16S rRNA genes. Further, the particle size distribution of (micro)aggregates in water was determined, with and without ultrasound treatment, as a measure of soil aggregate size distribution and stability.</p><p>Based on the first sampling campaign, we found that the overall prokaryotic community composition differed between the two sites, but not between plant species. Interdependencies between the community composition and EPS content were revealed, whereby soil organic matter (SOM) seems to be a regulating factor as increasing SOM contents resulted in more EPS-saccharides. Soil microaggregation in the topsoil was enhanced by the plant canopy, especially at the edge of <em>Macrochloa</em> tussocks. Contrary to the expectation that increasing inorganic C contents would diminish the importance of EPS, the parent material richest in inorganic C results in a significant effect of EPS-saccharides on microaggregation.</p><p>First results of the second sampling campaign indicate that even in the rhizoplane and rhizosphere, parent material had a dominating influence on the prokaryotic community composition. As EPS-saccharide contents and soil aggregation followed a similar decreasing trend with distance to the roots and canopy cover, interdependencies are expected.</p><p>From the outcomes until now, we can conclude that the availability of decomposable OM influences the prokaryotic community composition and thereby triggers EPS production, whereas large contents of polyvalent cations from carbonates promote the stabilizing effect of EPS on microaggregates.</p>


2019 ◽  
Vol 2 (1) ◽  
pp. 60-72 ◽  
Author(s):  
Bei Li ◽  
Jiwen Liu ◽  
Shun Zhou ◽  
Liang Fu ◽  
Peng Yao ◽  
...  

Abstract With the advantages of wide distribution, fast growth, and broad metabolic spectrum to organic carbon compounds, Vibrio may play an important role in organic carbon cycling. However, the ecological roles of Vibrio in many marine environments have not been explored. Here, the world’s deepest ‘blue hole’, the Sansha Yongle Blue Hole (SYBH) in the South China Sea, which is a geographically semi-enclosed environment featuring unique chemical characters, was investigated. The abundance, diversity and carbon source utilization capability of Vibrio were studied by quantification and high-throughput sequencing of Vibrio specific 16S rRNA genes and cultivation methods. The abundance of Vibrio in water column of the SYBH ranged from 3.78 × 104 to 7.35 × 106 16S rRNA gene copies L−1. Free-living Vibrio was more abundant than particle-associated Vibrio (~ 1.20 × 106 versus~ 2.68 × 105 gene copies L−1), indicating that Vibrio prefers a free-living life style. The Vibrio assemblages showed clear vertical stratification and could be divided into three groups: aerobic-transition, middle anaerobic and bottom anaerobic zones. Dissolved oxygen (DO), temperature, pH and salinity were the main environmental factors affecting the abundance and community composition. Cultivated Vibrio demonstrated a degrading capability to various macromolecular substrates, including starch, Tween 20/40/80, DNA, gelatin, alginate, casein, chitin, lecithin, κ-carrageenan, mannan, xylan and hyaluronic acid. This suggests that Vibrio could produce a variety of highly active extracellular enzymes. Our study provides new insights into the distribution pattern and possible role in carbon cycle of Vibrio in the unique environment of a ‘blue hole’.


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