Elevated functional versatility of the soil microbial community associated with the invader Carpobrotus edulis across a broad geographical scale

Caravaca, F.; Torres, Pilar Díez de Revenga; Díaz, G.; Roldán, A.

doi:10.1016/j.scitotenv.2021.152627

Cited by 9 publications

(6 citation statements)

References 51 publications

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“…Notably, each of the top 20 dominant bacterial metabolic pathways in JA have very approximate relative abundance with JB (Table 1 ), where biosynthesis pathways (12/20) are highly dominant. The biosynthesis pathways were also reported to be enriched in the rhizosphere microbiome of Barley ( Ye et al 2022 ) and Carpobrotus edulis ( Caravaca et al 2022 ). Interestingly, almost each pathway of these pathways exhibited an even relative abundance distribution (0.6-1.5%) in the rhizosphere bacterial communities.…”

Section: Resultsmentioning

confidence: 99%

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First insights into diversity and potential metabolic pathways of bacterial and fungal communities in the rhizosphere of Argemone mexicana L. (Papaveraceae) from the water-level-fluctuation zone of Wudongde Reservoir of the upper Yangtze river, China

Zhou¹,

Wu²,

Ma³

2023

BDJ

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The water-level fluctuation zone (WLFZ) of Wudongde reservoir of the upper Yangtze river is a completely new aquatic-terrestrial transitional zone, and its plant degenerate issue is attracting global concerns. Uncovering the unknown rhizosphere microbiome of dominant plants of this zone is helpful in understanding the plant-microbe interactions and their growth under the largely varying environment. Here, a first exploration of the rhizosphere bacterial and fungal communities of wilted (JB) and unwilted (JA) Argemone mexicana L. individuals from the WLFZ of Wudongde reservoir was carried out using high-throughput sequencing and MetaCyc metabolic pathway analyses. The results showed that rhizosphere of wilted A. mexicana L individuals exhibited a higher microbial richness and diversity than the unwilted ones, irrespective of the bacterial and fungal communities. It was noted that 837 common bacterial amplicon sequence variants (ASV) and 92 common fungal ASV were presented in both JA and JB with 3108 bacteria and 212 fungi unique to JA, and 3569 bacteria and 693 fungi unique to JB. Linear discriminant analysis effect Size (LEfSe) analyses indicated that the taxa that had the most contribution to observed differences between both JA and JB was Proteobacteria, Actinobacteria and Ascomycota for JA, and Bacteroidetes, Firmicutes, Verrucomicrobia, Basidiomycota and Ascomycota for JB. Organic compound conversion pathway (degradation/reduction/oxidation) was consistently highly represented in the rhizosphere microbiomes of both JA and JB. Overall, this study provides insights into the rhizosphere microbiome composition, diversity and metabolic pathways of both wilted and unwilted A. mexicana L. individuals in the WLFZ of Wudongde reservoir, and the results give valuable clues for manipulating microbes to support plant growth in such a recently-formed WLFZ under a dry-hot valley environment.

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Section: Resultsmentioning

confidence: 99%

“…The top 20 MetaCyc pathways in JA or JB are shown in Tables 1 , 2 . MetaCyc is a frequently-adopted database of metabolic pathways from all domains of life in the functional analyses of rhizosphere soils ( Caravaca et al 2022 , Jiménez et al 2020 ), covering 2749 pathways in the recent version ( Caspi et al 2020 ).…”

Section: Resultsmentioning

confidence: 99%

First insights into diversity and potential metabolic pathways of bacterial and fungal communities in the rhizosphere of Argemone mexicana L. (Papaveraceae) from the water-level-fluctuation zone of Wudongde Reservoir of the upper Yangtze river, China

Zhou¹,

Wu²,

Ma³

2023

BDJ

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“…Therefore, the FUNGuild database consolidated the published article data, followed by classification prediction . These included 12 categories: animal, plant, and wood-decaying fungi . The OTUs obtained by high-throughput sequencing were classified and identified, after which predictive analyses of their functions were conducted using the FAPROTAX () and FUNGuild () databases.…”

Section: Methodsmentioning

confidence: 99%

“…22 These included 12 categories: animal, plant, and wood-decaying fungi. 23 The OTUs obtained by high-throughput sequencing were classified and identified, after which predictive analyses of their functions were conducted using the FAPROTAX (http://www.cloud. biomicroclass.com/CloudPlatform/SoftPage/FAP) and FUN-Guild (http://www.funguild.org/) databases.…”

Section: Identification and Selection Of Bacteria And Fungimentioning

confidence: 99%

Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of Wheat Straw for Biogas Production via Anaerobic Digestion

Chen,

Cai,

Wang

et al. 2024

Environ. Sci. Technol.

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Biological pretreatment is a viable method for enhancing biogas production from straw crops, with the improvement in lignocellulose degradation efficiency being a crucial factor in this process. Herein, a metagenomic approach was used to screen core microorganisms (Bacillus subtilis, Acinetobacter johnsonii, Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading abilities among samples from three environments: pile retting wheat straw (WS), WS returned to soil, and forest soil. Subsequently, synthetic microbial communities were constructed for fermentation–enzyme production. The crude enzyme solution obtained was used to pretreat WS and was compared with two commercial enzymes. The synthetic microbial community enzyme-producing pretreatment (SMCEP) yielded the highest enzymatic digestion efficacy for WS, yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99, and 19.21%, respectively. Furthermore, pretreatment of WS with an enzyme solution, followed by anaerobic digestion achieved satisfactory results. SMCEP displayed the highest cumulative biogas production at 801.16 mL/g TS, which was 38.79% higher than that observed for WS, 22.15% higher than that of solid-state commercial enzyme pretreatment and 25.41% higher than that of liquid commercial enzyme pretreatment. These results indicate that enzyme-pretreated WS can significantly enhance biogas production. This study represents a solution to the environmental burden and energy use of crop residues.

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“…Our taxonomic analyses indicated that the phyla Proteobacteria (Pseudomonadota; from 39 to 43%), Actinobacteria (Actinomycetota; from 8 to 25%), and Bacteroidetes (Bacteroidota; from 13 to 17%) were the most abundant microbiota components in both studied compartments. Members of these phyla were observed as dominant taxa in the endosphere and rhizosphere of a great variety of plant species [24,56,57], including succulent plants such as Carpobrotus edulis, taxonomically related to sea fig, which showed relative abundances from 48 to 38% and from 29 to 27% for Proteobacteria and Actinobacteria in rhizosphere samples, respectively [24,58]. Moreover, Rodriguez-Caballero et al [59] reported that Actinobacteria (43%) and Proteobacteria (42%) were dominant taxa in the rhizosphere of C. edulis.…”

Section: Bacterial Communitiesmentioning

confidence: 99%

Bacterial Community Composition and Presence of Plasmids in the Endosphere- and Rhizosphere-Associated Microbiota of Sea Fig (Carpobrotus aequilaterus)

Sánchez-Salazar,

Acuña,

Sadowsky

et al. 2023

Diversity

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The plant microbiome is one of the most important environments for ecological interactions between bacteria that impact the plant and the ecosystem. However, studies on the diversity of mobile genetic elements (such as plasmids) associated with the plant microbiome are very scarce. Here, we determined the bacterial community composition and the occurrence of plasmids in the microbiota associated with sea fig, Carpobrotus aequilaterus (N.E. Br.), a succulent species widely used as an ornamental plant in Chile. The abundance and composition of the endophytic and rhizospheric bacterial communities were determined by quantitative PCR (qPCR) and DNA metabarcoding analysis. Plasmid diversity in the plant microbiome was determined by plasmid DNA extraction and screened by endpoint PCR of backbone genes for four different incompatibility groups (Inc). The results showed about 106 copies of the 16S rRNA gene in the endosphere and rhizosphere, showing significant differences according to the diversity index. Proteobacteria (Pseudomonadota; 43.4%), Actinobacteria (Actinomycetota; 25.7%), and Bacteroidetes (Bacteroidota; 17.4%) were the most dominant taxa in both plant compartments, and chemoheterotrophy (30%) was the main predicted function assigned to the microbiota. Plasmid diversity analysis showed the presence of transferable plasmids in the endosphere and rhizosphere of C. aequilaterus, particularly among environmental plasmids belonging to the IncP and IncN incompatibility groups.

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Elevated functional versatility of the soil microbial community associated with the invader Carpobrotus edulis across a broad geographical scale

Cited by 9 publications

References 51 publications

First insights into diversity and potential metabolic pathways of bacterial and fungal communities in the rhizosphere of Argemone mexicana L. (Papaveraceae) from the water-level-fluctuation zone of Wudongde Reservoir of the upper Yangtze river, China

First insights into diversity and potential metabolic pathways of bacterial and fungal communities in the rhizosphere of Argemone mexicana L. (Papaveraceae) from the water-level-fluctuation zone of Wudongde Reservoir of the upper Yangtze river, China

Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of Wheat Straw for Biogas Production via Anaerobic Digestion

Bacterial Community Composition and Presence of Plasmids in the Endosphere- and Rhizosphere-Associated Microbiota of Sea Fig (Carpobrotus aequilaterus)

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