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Article: PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases

Costa, Ohana Y. A. / de Hollander, Mattias / Kuramae, Eiko E. / Bodelier, Paul L. E.

Microorganisms. 2022 May 25, v. 10, no. 6

2022

Abstract: The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a ... ...

Abstract	The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.
Keywords	computer software ; data collection ; genes ; phylogeny
Language	English
Dates of publication	2022-0525
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms10061093
Database	NAL-Catalogue (AGRICOLA)

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Article: PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases.

Costa, Ohana Y A / de Hollander, Mattias / Kuramae, Eiko E / Bodelier, Paul L E

Microorganisms

2022 Volume 10, Issue 6

Abstract	The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.
Language	English
Publishing date	2022-05-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms10061093
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.

Costa, Ohana Y A / de Hollander, Mattias / Pijl, Agata / Liu, Binbin / Kuramae, Eiko E

Microbiome

2020 Volume 8, Issue 1, Page(s) 76

Abstract: Background: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and ... ...

Abstract	Background: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics. Results: SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases. Conclusions: We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.
MeSH term(s)	Bacteria/enzymology ; Bacteria/genetics ; Biodegradation, Environmental ; Metagenome ; Metagenomics ; Microbiota/genetics ; Polymers/metabolism
Chemical Substances	Polymers
Language	English
Publishing date	2020-06-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-020-00836-7
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Article ; Online: Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.

Costa, Lilian S Abreu Soares / de Faria, Mírian Rabelo / Chiaramonte, Josiane Barros / Mendes, Lucas W / Sepo, Edis / de Hollander, Mattias / Fernandes, José Maurício Cunha / Carrión, Víctor J / Bettiol, Wagner / Mauchline, Tim H / Raaijmakers, Jos M / Mendes, Rodrigo

Environmental microbiome

2023 Volume 18, Issue 1, Page(s) 85

Abstract: Background: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. ... ...

Abstract	Background: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. Results: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides. Conclusion: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.
Language	English
Publishing date	2023-12-05
Publishing country	England
Document type	Journal Article
ISSN	2524-6372
ISSN (online)	2524-6372
DOI	10.1186/s40793-023-00529-2
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Article ; Online: Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.

Mendes, Lucas William / Raaijmakers, Jos M / de Hollander, Mattias / Sepo, Edis / Gómez Expósito, Ruth / Chiorato, Alisson Fernando / Mendes, Rodrigo / Tsai, Siu Mui / Carrión, Victor J

Environmental microbiome

2023 Volume 18, Issue 1, Page(s) 68

Abstract: Background: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their ... ...

Abstract	Background: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar. Results: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion. Conclusion: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.
Language	English
Publishing date	2023-08-03
Publishing country	England
Document type	Journal Article
ISSN	2524-6372
ISSN (online)	2524-6372
DOI	10.1186/s40793-023-00524-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The wild side of plant microbiomes.

Pérez-Jaramillo, Juan E / Carrión, Víctor J / de Hollander, Mattias / Raaijmakers, Jos M

Microbiome

2018 Volume 6, Issue 1, Page(s) 143

MeSH term(s)	Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Domestication ; Microbiota ; Phylogeny ; Plant Roots/microbiology ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA
Chemical Substances	DNA, Bacterial ; DNA, Ribosomal ; RNA, Ribosomal, 16S
Language	English
Publishing date	2018-08-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-018-0519-z
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Article ; Online: Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input

Leite, Marcio F.A. / Dimitrov, Mauricio R. / Freitas-Iório, Raquel P. / de Hollander, Mattias / Cipriano, Matheus A.P. / Andrade, Sara A.L. / da Silveira, Adriana P.D. / Kuramae, Eiko E.

Science of the Total Environment. 2021 Dec., v. 800 p.149493-

2021

Abstract: The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable ... ...

Abstract	The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.
Keywords	Herbaspirillum frisingense ; Paraburkholderia ; Pseudomonas fluorescens ; biomass ; crop production ; environment ; genetic background ; microbiome ; nitrogen ; nutrient uptake ; prokaryotic cells ; rhizosphere ; soil ; sugarcane ; Endosphere ; Prokaryote community ; Macronutrient ; Micronutrient ; Plant nutrient use efficiency ; Beneficial bacteria
Language	English
Dates of publication	2021-12
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2021.149493
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia.

Pérez-Jaramillo, Juan E / de Hollander, Mattias / Ramírez, Camilo A / Mendes, Rodrigo / Raaijmakers, Jos M / Carrión, Víctor J

Microbiome

2019 Volume 7, Issue 1, Page(s) 114

Abstract: Background: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.: Results: ... ...

Abstract	Background: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. Results: Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. Conclusions: Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.
MeSH term(s)	Bacteria/isolation & purification ; Colombia ; Domestication ; Microbiota ; Phaseolus/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Soil/chemistry ; Soil Microbiology
Chemical Substances	Soil
Language	English
Publishing date	2019-08-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-019-0727-1
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Article ; Online: Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input.

Leite, Marcio F A / Dimitrov, Mauricio R / Freitas-Iório, Raquel P / de Hollander, Mattias / Cipriano, Matheus A P / Andrade, Sara A L / da Silveira, Adriana P D / Kuramae, Eiko E

The Science of the total environment

2021 Volume 800, Page(s) 149493

Abstract	The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.
MeSH term(s)	Bacteria ; Burkholderiaceae ; Enterobacteriaceae ; Herbaspirillum ; Nitrogen ; Plant Roots ; Rhizosphere ; Saccharum ; Soil Microbiology
Chemical Substances	Nitrogen (N762921K75)
Language	English
Publishing date	2021-08-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2021.149493
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Article: Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System.

Lupatini, Manoeli / Korthals, Gerard W / de Hollander, Mattias / Janssens, Thierry K S / Kuramae, Eiko E

Frontiers in microbiology

2017 Volume 7, Page(s) 2064

Abstract: Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited ... ...

Abstract	Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.
Language	English
Publishing date	2017-01-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2016.02064
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