Deciphering the succession dynamics of dominant and rare genera in biofilm development process

Yuan, Shasha; Yu, Ziquan; Pan, Siyi; Huang, Jiamei; Meng, Fangang

doi:10.1016/j.scitotenv.2020.139961

Cited by 13 publications

(5 citation statements)

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“…However, shoots dominant genera were while Achromobacter , Alloprevotella , and Enterobacter . Similar results were also reported by previous studies ( Miri et al, 2019 ; Yuan et al, 2020 ). Since leaves and roots, rhizosphere soils have the highest bacterial community richness and diversity, according to an alpha diversity analysis.…”

Section: Discussionsupporting

confidence: 93%

Biological functions of endophytic bacteria in Robinia pseudoacacia ‘Hongsen’

Huang,

Chen,

et al. 2023

Front. Microbiol.

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IntroductionEndophytes and their host plants have co-evolved for a very long time. This relationship has led to the general recognition of endophytes as a particular class of microbial resources. R. pseudoacacia ‘Hongsen’ is drought- and barren-resistant species that can be grown in both the north and south of China, efficiently addresses the ecological issues caused by China’s ‘southern eucalyptus and northern poplar. Up to date, cultured-dependent studies are available for the R. pseudoacacia nitrogen-fixing and other endophytes. Therefore, the present research studied the R. pseudoacacia ‘Hongsen,’ microbiome in detail by high-throughput sequencing and culture dependant.MethodsThis study examined microbial species and functional diversity in Robinia pseudoacacia ‘Hongsen’ using culture-dependent (isolation) and culture-independent techniques.ResultsA total of 210 isolates were isolated from R. pseudoacacia ‘Hongsen.’ These isolates were clustered into 16 groups by the In Situ PCR (IS-PCR) fingerprinting patterns. 16S rRNA gene sequence analysis of the representative strain of each group revealed that these groups belonged to 16 species of 8 genera, demonstrating the diversity of endophytes in R. pseudoacacia ‘Hongsen’. ’Bacillus is the most prevalent genus among all the endophytic bacteria. High-throughput sequencing of endophytic bacteria from R. pseudoacacia ‘Hongsen’ of the plant and the rhizosphere soil bacteria showed that the bacterial populations of soil near the root, leaf, and rhizosphere differed significantly. The microbial abundance decreased in the endophytes as compared to the rhizosphere. We observed a similar community structure of roots and leaves. With and without root nodules, Mesorhizobium sp. was significantly different in R. pseudoacacia ‘Hongsen’ plant.DiscussionIt was predicted that R. pseudoacacia ‘Hongsen’ plant endophytic bacteria would play a significant role in the metabolic process, such as carbohydrate metabolism, amino acid metabolism, membrane transport, and energy metabolism.

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Section: Discussionsupporting

confidence: 93%

Biological functions of endophytic bacteria in Robinia pseudoacacia ‘Hongsen’

Huang,

Chen,

et al. 2023

Front. Microbiol.

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“…To detect taxonomic variability among different treatments and XR samples, a least discriminant analysis (LDA) was conducted to recognize biomarkers (threshold > 4.0) 50 . The co-occurrence networks were performed by calculating the Spearman’s rank correlations with the psych package based on the relative abundance of genera, with |ρ| greater than 0.6 and a p value of less than 0.05, using Gephi (v. 0.9.2) 51 . The linear least-squares regression mode was used to identify the correlation between α-diversity of both macrobenthos and microbial community (ASV richness and Shannon index) and to assess the persistence of the relative abundance of dominant phyla over time.…”

Section: Methodsmentioning

confidence: 99%

Microbial community shift on artificial biological reef structures (ABRs) deployed in the South China Sea

Mohamed

Abd‐Elgawad

Cai

et al. 2023

Sci Rep

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Many Artificial Reefs (ARs) have been used worldwide for marine habitat and coral reef restoration. However, the microbial community structure that colonize the ARs and their progressive development have been seldom investigated. In this study, the successive development of the microbial communities on environmentally friendly Artificial Biological Reef structures (ABRs)R made of special concrete supported with bioactive materials collected from marine algal sources were studied. Three seasons (spring, summer and autumn), three coral reef localities and control models (SCE) without bioactive material and (NCE) made of normal cement were compared. The structure of the microbial pattern exhibited successive shifts from the natural environment to the ABRs supported with bioactive materials (ABAM). Cyanobacteria, Proteobacteria, and Planctomycetota were shown to be the most three dominant phyla. Their relative abundances pointedly increased on ABAM and SCE models compared to the environment. Amplicon Sequence Variant (ASV) Richness and Shannon index were obviously higher on ABAM models and showed significant positive relationship with that of macrobenthos than those on the controls and the natural reef (XR). Our results offer successful establishment of healthy microbial films on the ABR surfaces enhanced the restoration of macrobenthic community in the damaged coral reefs which better understands the ecological role of the ABRs.

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“…Many prokaryotic taxa in biofilms associated with high-settlement were found at very low abundances, supporting previous hypotheses that low-abundance taxa may be capable of inducing larval settlement [ 21 , 50 ]. Rare taxa (<1% relative abundance) often show positive interactions with each other in developing biofilms [ 51 ] via cross-feeding [ 52 ] and sharing metabolites [ 53 ], and can play an integral role in shaping biofilm communities [ 54 ]. The addition of these rare taxa in a multi-species community could create a community niche with new interrelated functions [ 55 ] that may support pathways and functions necessary to induce larval settlement.…”

Section: Discussionmentioning

confidence: 99%

Linking differences in microbial network structure with changes in coral larval settlement

Turnlund,

Vanwonterghem,

Botté

et al. 2023

ISME Communications

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Coral cover and recruitment have decreased on reefs worldwide due to climate change-related disturbances. Achieving reliable coral larval settlement under aquaculture conditions is critical for reef restoration programmes; however, this can be challenging due to the lack of reliable and universal larval settlement cues. To investigate the role of microorganisms in coral larval settlement, we undertook a settlement choice experiment with larvae of the coral Acropora tenuis and microbial biofilms grown for different periods on the reef and in aquaria. Biofilm community composition across conditioning types and time was profiled using 16S and 18S rRNA gene sequencing. Co-occurrence networks revealed that strong larval settlement correlated with diverse biofilm communities, with specific nodes in the network facilitating connections between modules comprised of low- vs high-settlement communities. Taxa associated with high-settlement communities were identified as Myxoccales sp., Granulosicoccus sp., Alcanivoraceae sp., unassigned JTB23 sp. (Gammaproteobacteria), and Pseudovibrio denitrificans. Meanwhile, taxa closely related to Reichenbachiella agariperforans, Pleurocapsa sp., Alcanivorax sp., Sneathiella limmimaris, as well as several diatom and brown algae were associated with low settlement. Our results characterise high-settlement biofilm communities and identify transitionary taxa that may develop settlement-inducing biofilms to improve coral larval settlement in aquaculture.

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Deciphering the succession dynamics of dominant and rare genera in biofilm development process

Cited by 13 publications

References 58 publications

Biological functions of endophytic bacteria in Robinia pseudoacacia ‘Hongsen’

Biological functions of endophytic bacteria in Robinia pseudoacacia ‘Hongsen’

Microbial community shift on artificial biological reef structures (ABRs) deployed in the South China Sea

Linking differences in microbial network structure with changes in coral larval settlement

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