Metaproteomics reveals the structural and functional diversity of Dermatocarpon miniatum (L.) W. Mann. Microbiota

Ullah, Junaid; Khanum, Zainab Khanum Zainab; Khan, Iltaf; Khalid, Abdul Nasir; Musharraf, Syed Ghulam; Ali, Asghar

doi:10.1016/j.funbio.2020.10.001

Cited by 4 publications

(3 citation statements)

References 36 publications

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“…In this respect, the lichen microbiome can be studied using a diverse spectrum of 'omics' technologies (Figure 4). Despite metagenomic analyses (e.g., Grube et al, 2015;Cernava et al, 2015;Aschenbrenner et al, 2017;Cernava et al, 2018;Graham et al, 2018), many studies applied metatranscriptomic (e.g., Cernava et al, 2017Cernava et al, , 2019 and metaproteomic (e.g., Berg et al, 2011;Schneider et al, 2011;Grube et al, 2015;Cernava et al, 2017;Eymann et al, 2017;Ullah et al, 2020) approaches to study lichen symbioses.…”

Section: Molecular Tools To Investigate Lichen-associated Microorganismsmentioning

confidence: 99%

The Lichens’ Microbiota, Still a Mystery?

Grimm¹,

et al. 2021

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Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont’s contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.

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Section: Molecular Tools To Investigate Lichen-associated Microorganismsmentioning

confidence: 99%

The Lichens’ Microbiota, Still a Mystery?

Grimm¹,

et al. 2021

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“…Since many of the detected microorganisms have not been successfully isolated and cultured, subsequent culture methods can be improved, including low temperature and acid enrichment (Biosca et al, 2016). We can further reveal the metabolic activity and function of endophytes in lichens through multiple omics techniques, containing metabolomics, transcriptomics, and metaproteomics (Nazem-Bokaee et al, 2021;Ullah et al, 2021). Moreover, our samples were collected in Tibet, a typical high altitude region with obvious freezing-thawing stress, which may affect the structural changes of endophytes in lichens (Leiva et al, 2021).…”

Section: A B C Dmentioning

confidence: 99%

Diversity of endophytic bacterial and fungal microbiota associated with the medicinal lichen Usnea longissima at high altitudes

Wang

Li²,

Yang³

et al. 2022

Front. Microbiol.

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Endophytic microbial communities of lichen are emerging as novel microbial resources and for exploration of potential biotechnological applications. Here, we focused on a medicinal lichen Usnea longissima, and investigated its bacterial and fungal endophytes. Using PacBio 16S rRNA and ITS amplicon sequencing, we explored the diversity and composition of endophytic bacteria and fungi in U. longissima collected from Tibet at five altitudes ranging from 2,989 to 4,048 m. A total of 6 phyla, 12 classes, 44 genera, and 13 species of the bacterial community have been identified in U. longissima. Most members belong to Alphaproteobacteria (42.59%), Betaproteobacteria (33.84%), Clostridia (13.59%), Acidobacteria (7%), and Bacilli (1.69%). As for the fungal community, excluding the obligate fungus sequences, we identified 2 phyla, 15 classes, 65 genera, and 19 species. Lichen-related fungi of U. longissima mainly came from Ascomycota (95%), Basidiomycota (2.69%), and unidentified phyla (2.5%). The presence of the sequences that have not been characterized before suggests the novelty of the microbiota. Of particular interest is the detection of sequences related to lactic acid bacteria and budding yeast. In addition, the possible existence of harmful bacteria was also discussed. To our best knowledge, this is the first relatively detailed study on the endophytic microbiota associated with U. longissima. The results here provide the basis for further exploration of the microbial diversity in lichen and promote biotechnological applications of lichen-associated microbial strains.

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“…By characterizing changes in the diversity and functional capacity of microbial communities over time and space, metaproteomics can help us understand how microbes influence and respond to chemical, physical and biological perturbations in the diverse niches they occupy, including nutrient fluxes (Mikan et al, 2020), anthropogenic pollution (Bargiela et al, 2015), and phage attack (Heyer, Schallert, Siewert, et al, 2019). Metaproteomics has been applied to the study of microbial communities from diverse aquatic and terrestrial environments, including river sediment, Antarctic coastal waters, wastewater treatment plants, thermal vents, hot and polar deserts, and in symbiotic relationships with higher‐order organisms (Fernández‐Martínez et al, 2019; Pjevac et al, 2018; Rodríguez‐Ramos et al, 2022; Ullah et al, 2021; Zampieri et al, 2016). The power and utility of this emerging technology make it an attractive complement to nucleic acid‐based approaches and conventional physiological studies.…”

Section: Introductionmentioning

confidence: 99%

Critical steps in an environmental metaproteomics workflow

Nebauer,

Pearson,

Neilan

2024

Environmental Microbiology

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Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non‐expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high‐quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single‐organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.

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Metaproteomics reveals the structural and functional diversity of Dermatocarpon miniatum (L.) W. Mann. Microbiota

Cited by 4 publications

References 36 publications

The Lichens’ Microbiota, Still a Mystery?

The Lichens’ Microbiota, Still a Mystery?

Diversity of endophytic bacterial and fungal microbiota associated with the medicinal lichen Usnea longissima at high altitudes

Critical steps in an environmental metaproteomics workflow

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