Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria
Authors: Tomislav Cernava
Christian Berg
Wisnu Adi Wicaksono
Gabriele Berg
Journal: Microbiome (2021)
Discipline: MICROBIOLOGY
Keywords: Bog ecosystems; Bryophytes; Coevolution; Microbiome; Vascular plants.
Affiliations: Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria., Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria. ., Institute of Plant Sciences, University of Graz, Graz, Austria.

Abstract:  Background: Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant-microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant-microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem. Results: Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens. Conclusions: The unexpectedly high specificity of the plant microbiota reflects intimate plant-microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant-microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant-microbe coevolution. Video abstract. 

Retracted: No

PubPeer comments:
 Availability of data?  This shotgun metagenome project has been deposited in the European Nucleotide Archive (ENA) database under the study number PRJEB39100 and accession numbers ERR4298333 and ERR4298344. Seven datasets are not available on ENA: ERR4298333, ERR4298336, ERR4298337, ERR4298338, ERR4298341, ERR4298342, ERR4298344. , 
 #1 Explain the issue in more detail. I have checked the availbility and the data is publicly accessible under the provided accession numbers. For example ERR4298333 can be reached without any problems: https: trace.ncbi.nlm.nih.gov Traces sra ?run=ERR4298333 , 
 #1 I have checked again and your issue seems to be that when accessed via the ENA browser, the option  ftp download is not available. However, each of the files is available for regular download. In summary, all of our data is publicly available, but you should check with ENA s technical support if you need the ftp download option.It is something that we cannot influence. , 
 #2 According to the ENA file report for the project: PRJEB39100 the column fastq for e.g. ERR4298333 is empty. I was able to download the original data files but I am not sure what  quality_filtered.fastqsanger.gz.1 means exactly. I assume the HiSeq 2500 raw data was subject to adaptor trimming and quality filtering as described in the article:  Based on the results, quality filtering was subsequently performed using Trimmomatic v0.39 and VSEARCH v2.14.2 to remove Illumina adaptor and low-quality reads (Phredu2009 u200920), respectively. Would you be able to share the command lines for the cleaning steps? java -jar trimmomatic-0.39.jar ??? vsearch ??? Thanks! ,