Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities, and prokaryotic community profiles in Argentinean semi-arid soils

2021 ◽  
Author(s):  
L A Gabbarini ◽  
E Figuerola ◽  
J P Frene ◽  
N B Robledo ◽  
F M Ibarbalz ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Structure ◽  
Management Practices ◽  
Soil Health ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Prokaryotic Community ◽  
C Cycle

Abstract The effects of tillage on soil structure, physiology, and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs. no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles, and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analysed at two soil depths (0–5, 5–10 cm) in samples taken 6, 18, and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils thirty months after switching from CT to NT. Bacteria and Archaea OTUs, which responded to NT were associated with coarse soil fraction, SOC and C cycle enzymes while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.

scholarly journals Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Niclas Lampert ◽  
Aram Mikaelyan ◽  
Andreas Brune
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Community Structure ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Feeding Groups ◽  
Reducing Conditions ◽  
Primary Driver

Abstract Background Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter. Results The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites. Conclusion Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.

scholarly journals Assessment of total bacterial diversity in whiteleg shrimps and its aquaculture environment in Pangkajene and Banyuwangi, Indonesia

2021 ◽  
pp. 26-37
Author(s):  
Yuni Puji Hastuti ◽  
Yuli Siti Fatma ◽  
Hardi Pitoyo ◽  
Wildan Nurussalam ◽  
Jajang Ruhyana
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Community Structure ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Sequencing Platform ◽  
The Difference

Detection of bacterial diversity in whiteleg shrimps and its rearing water is a vital first step in monitoring aquaculture activities. Bacterial community imbalance in whiteleg shrimps and its rearing water influences the quality and quantity of shrimp production. Identifying the bacterial community provides basic information related to dominant bacterial groups in whiteleg shrimps and environments, providing recommendations for proper environmental monitoring and management. In this study, we investigated bacterial community structure in the rearing water and intestinal tract of whiteleg shrimp (Litopenaeus vannamei) collected from two sites, i.e., Pangkajene, South Sulawesi (SU) and Banyuwangi, East Java (BW), Indonesia. The bacterial community was analyzed using amplicon sequencing with Illumina sequencing platform based on the V3-V4 region of the 16S rRNA genes. Bacterial diversity and composition were found differed between the rearing water and the shrimps’ intestines. Bacterial diversity in the rearing water of Banyuwangi (W.BW) was higher than that of Pangkajene (W.SU). Proteobacteria, Bacteroidetes, and Firmicutes were found as the most dominant phyla in rearing water from both farms, while distinct bacterial composition was observed in the shrimps’ intestines. The shrimp intestine from Banyuwangi (U.BW) was dominated by Firmicutes (22.36%), Proteobacteria (22.33%), and Verrucomicrobia (21.11%). In contrast, the shrimp intestine from Pangkajene (U.SU) was highly dominated by Tenericutes (88.54%), followed by Proteobacteria (4.66%), and Firmicutes (2.27%). The difference in bacterial community structure between the rearing water and shrimps’ intestines suggested that the host intestinal environment might have greater selective pressure for bacterial composition inhabiting L.vannamei intestines. Our observations suggest that the shrimps cultured in the rearing water with the similar dominant bacterial group have specific intestinal bacterial diversity.

scholarly journals Coordination of microbe–host homeostasis by crosstalk with plant innate immunity

Nature Plants ◽  
2021 ◽  
Author(s):  
Ka-Wai Ma ◽  
Yulong Niu ◽  
Yong Jia ◽  
Jana Ordon ◽  
Charles Copeland ◽  
...  
Keyword(s):  
Growth Inhibition ◽  
Amplicon Sequencing ◽  
Host Susceptibility ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Root Growth Inhibition ◽  
Natural Soil ◽  
Molecular Pattern ◽  
Immune Related Genes ◽  
Molecular Patterns

AbstractPlants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth–defence trade-off. Here, we report that, in monoassociations, 41% (62 out of 151) of taxonomically diverse root bacterial commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacterial 16S rRNA genes reveals that immune activation alters the profile of synthetic communities (SynComs) comprising RGI-non-suppressive strains, whereas the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes, with functions related to root development and nutrient transport. Furthermore, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Precolonization of plants with RGI-suppressive SynComs, or mutation of one commensal-downregulated transcription factor, MYB15, renders the plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and RGI-suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defence-associated growth inhibition, ultimately leading to commensal–host homeostasis.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

scholarly journals Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yusuke Okazaki ◽  
Shohei Fujinaga ◽  
Michaela M. Salcher ◽  
Cristiana Callieri ◽  
Atsushi Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Regional Scale ◽  
Scale Up ◽  
Amplicon Sequencing ◽  
Freshwater Ecosystems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Long Read

Abstract Background Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Results Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Conclusions Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future.

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Doreen Babin ◽  
Loreen Sommermann ◽  
Soumitra Paul Chowdhury ◽  
Jan H Behr ◽  
Martin Sandmann ◽  
...  
Keyword(s):  
Growth Regulators ◽  
Stress Responses ◽  
Crop Production ◽  
Agricultural Management ◽  
Plant Performance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Microbiota ◽  
Sustainable Crop Production

ABSTRACT A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.

Effect of long-term nutrient management practices on soil health and paddy yield of rice-rice-fallow cropping system in tropic humid climate

2021 ◽  
Vol 107 ◽  
pp. 103362
Author(s):  
Umme Aminun Naher ◽  
Md Mozammel Haque ◽  
Faruk Hossain Khan ◽  
Md Imran Ullah Sarkar ◽  
Tahmid Hossain Ansari ◽  
...  
Keyword(s):  
Management Practices ◽  
Nutrient Management ◽  
Soil Health ◽  
Cropping System ◽  
Humid Climate ◽  
Paddy Yield

scholarly journals Soil structure after 18 years of long-term different tillage systems and fertilisation in Haplic Luvisol

2018 ◽  
Vol 13 (No. 3) ◽  
pp. 140-149 ◽  
Author(s):  
Šimanský Vladimír ◽  
Lukáč Martin
Keyword(s):  
Organic Matter ◽  
Soil Structure ◽  
Management Practices ◽  
Crop Residues ◽  
Organic Matter Content ◽  
Matter Content ◽  
Soil Tillage ◽  
Arable Soils ◽  
Water Stable Aggregates

Soil structure is a key determinant of many soil environmental processes and is essential for supporting terrestrial ecosystem productivity. Management of arable soils plays a significant role in forming and maintaining their structure. Between 1994 and 2011, we studied the influence of soil tillage and fertilisation regimes on the stability of soil structure of loamy Haplic Luvisol in a replicated long-term field experiment in the Dolná Malanta locality (Slovakia). Soil samples were repeatedly collected from plots exposed to the following treatments: conventional tillage (CT) and minimum tillage (MT) combined with conventional (NPK) and crop residue-enhanced fertilisation (CR+NPK). MT resulted in an increase of critical soil organic matter content (St) by 7% in comparison with CT. Addition of crop residues and NPK fertilisers significantly increased St values (by 7%) in comparison with NPK-only treatments. Soil tillage and fertilisation did not have any significant impact on other parameters of soil structure such as dry sieving mean weight diameters (MWD), mean weight diameter of water-stable aggregates (MWD<sub>WSA</sub>), vulnerability coefficient (Kv), stability index of water-stable aggregates (Sw), index of crusting (Ic), contents of water-stable macro- (WSA<sub>ma</sub>) and micro-aggregates (WSA<sub>mi</sub>). Ic was correlated with organic matter content in all combinations of treatments. Surprisingly, humus quality did not interact with soil management practices to affect soil structure parameters. Higher sums of base cations, CEC and base saturation (Bs) were linked to higher Sw values, however higher values of hydrolytic acidity (Ha) resulted in lower aggregate stability in CT treatments. Higher content of K<sup>+</sup> was responsible for higher values of MWD<sub>WSA </sub>and MWD in CT. In MT, contents of Ca<sup>2+</sup>, Mg<sup>2+ </sup>and Na<sup>+</sup> were significantly correlated with contents of WSA<sub>mi </sub>and WSA<sub>ma</sub>. Higher contents of Na<sup>+</sup> negatively affected St values and positive correlations were detected between Ca<sup>2+</sup>, Mg<sup>2+ </sup>and Na<sup>+</sup> and Ic in NPK treatments.

scholarly journals The Response of the Soil Microbiota to Long-Term Mineral and Organic Nitrogen Fertilization is Stronger in the Bulk Soil than in the Rhizosphere

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 456 ◽  
Author(s):  
Massimiliano Cardinale ◽  
Stefan Ratering ◽  
Aitak Sadeghi ◽  
Sushil Pokhrel ◽  
Bernd Honermeier ◽  
...  
Keyword(s):  
N Fertilization ◽  
16S Rrna Genes ◽  
Bulk Soil ◽  
Rrna Genes ◽  
Soil Microbiome ◽  
Future Research ◽  
Arable Soils ◽  
Mineral N ◽  
Bacterial Microbiota

The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA, nirK, nirS, nosZ-I and nosZ-II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales), and a bulk soil cluster, dominated by Acidobacteria, Gemmatominadetes and “Latescibacteria” (hub taxa: Acidobacteria). In the bulk soil, mineral N-fertilization reduced nirK, amoA, nosZ-I and nosZ-II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.

Sign in / Sign up

Export Citation Format

Share Document