1
|
Clinton M, Wyness AJ, Martin SAM, Brierley AS, Ferrier DEK. Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study. BMC Vet Res 2024; 20:340. [PMID: 39090695 PMCID: PMC11293161 DOI: 10.1186/s12917-024-04125-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Understanding the relationship between resident microbiota and disease in cultured fish represents an important and emerging area of study. Marine gill disorders in particular are considered an important challenge to Atlantic salmon (Salmo salar) aquaculture, however relatively little is known regarding the role resident gill microbiota might play in providing protection from or potentiating different gill diseases. Here, 16S rRNA sequencing was used to examine the gill microbiome alongside fish health screening in farmed Atlantic salmon. Results were used to explore the relationship between microbial communities and gill disease. RESULTS Microbial community restructuring was observed throughout the sampling period and linked to varied drivers of change, including environmental conditions and severity of gill pathology. Taxa with significantly greater relative abundance on healthier gills included isolates within genus Shewanella, and taxa within family Procabacteriaceae. In contrast, altered abundance of Candidatus Branchiomonas and Rubritalea spp. were associated with damaged gills. Interestingly, more general changes in community richness and diversity were not associated with altered gill health, and thus not apparently deleterious to fish. Gross and histological gill scoring demonstrated seasonal shifts in gill pathology, with increased severity of gill damage in autumn. Specific infectious causes that contributed to observed pathology within the population included the gill disorder amoebic gill disease (AGD), however due to the uncontrolled nature of this study and likely mixed contribution of various causes of gill disease to observed pathology results do not strongly support an association between the microbial community and specific infectious or non-infectious drivers of gill pathology. CONCLUSIONS Results suggest that the microbial community of farmed Atlantic salmon gills undergo continual restructuring in the marine environment, with mixed influences upon this change including environmental, host, and pathogenic factors. A significant association of specific taxa with different gill health states suggests these taxa might make meaningful indicators of gill health. Further research with more frequent sampling and deliberate manipulation of gills would provide important advancement of knowledge in this area. Overall, although much is still to be learnt regarding what constitutes a healthy or maladapted gill microbial community, the results of this study provide clear advancement of the field, providing new insight into the microbial community structure of gills during an annual production cycle of marine-stage farmed Atlantic salmon.
Collapse
Affiliation(s)
- Morag Clinton
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK.
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Sitka Sound Science Center, Alaska, Sitka, USA.
| | - Adam J Wyness
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK
- Scottish Association for Marine Science, Oban, UK
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, University of Aberdeen, Aberdeen, UK
| | | | - David E K Ferrier
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK.
| |
Collapse
|
2
|
Marzinelli EM, Thomas T, Vadillo Gonzalez S, Egan S, Steinberg PD. Seaweeds as holobionts: Current state, challenges, and potential applications. JOURNAL OF PHYCOLOGY 2024. [PMID: 39047050 DOI: 10.1111/jpy.13485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
Seaweeds play a strong ecological and economical role along the world's coastlines, where they support industries (e.g., aquaculture, bioproducts) and essential ecosystem services (e.g., biodiversity, fisheries, carbon capture). Evidence from wild and cultured seaweeds suggests that microorganisms play crucial roles in their health and functioning, prompting the need for considering seaweeds and their microbiome as a coherent entity or "holobiont." Here we show that the number of studies investigating seaweed hosts and their microbiome have increased in the last two decades. This likely reflects the increase in the appreciation of the importance of microbiomes for eukaryotic hosts, improved molecular approaches used to characterize their interactions, and increasing interest in commercial use of seaweeds. However, although increasing, most studies of seaweed holobionts have focused on (i) a few seaweed species of ecological or commercial significance, (ii) interactions involving only bacteria, and (iii) descriptive rather than experimental approaches. The relatively few experimental studies have mostly focused on manipulating abiotic factors to examine responses of seaweeds and their microbiome. Of the few studies that directly manipulated microorganisms to investigate their effects on seaweeds, most were done in laboratory or aquaria. We emphasize the need to move beyond the descriptions of patterns to experimental approaches for understanding causation and mechanisms. We argue that such experimental approaches are necessary for a better understanding of seaweed holobionts, for management actions for wild and cultivated seaweeds, and to better integrate studies of seaweed holobionts with the broader fields of seaweed ecology and biology, which are strongly experimental.
Collapse
Affiliation(s)
- Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sebastian Vadillo Gonzalez
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter D Steinberg
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
3
|
Palanikumar I, Sinha H, Raman K. Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models. iScience 2024; 27:110358. [PMID: 39092173 PMCID: PMC11292516 DOI: 10.1016/j.isci.2024.110358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/10/2024] [Accepted: 06/20/2024] [Indexed: 08/04/2024] Open
Abstract
Utilization of 16S rRNA data in constraint-based modeling to characterize microbial communities confronts a major hurdle of lack of species-level resolution, impeding the construction of community models. We introduce "Panera," an innovative framework designed to model communities under this uncertainty and yet perform metabolic inferences using pan-genus metabolic models (PGMMs). We demonstrated PGMMs' utility for comprehending the metabolic capabilities of a genus and in characterizing community models using amplicon data. The unique, adaptable nature of PGMMs unlocks their potential in building hybrid communities, combining genome-scale metabolic models (GSMMs) and PGMMs. Notably, these models provide predictions comparable to the standard GSMM-based community models, while achieving a nearly 46% reduction in error compared to the genus model-based communities. In essence, "Panera" presents a potent and effective approach to aid in metabolic modeling by enabling robust predictions of community metabolic potential when dealing with amplicon data, and offers insights into genus-level metabolic landscapes.
Collapse
Affiliation(s)
- Indumathi Palanikumar
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
- Department of Data Science and AI, Wadhwani School of Data Science and AI, IIT Madras, Chennai 600 036, India
| |
Collapse
|
4
|
Melchior PP, Reiss E, Payne Z, Vuong N, Hovorka K, Lindsay HL, Diaz GR, Gaire T, Noyes N. Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season. PLoS One 2024; 19:e0306602. [PMID: 38995889 PMCID: PMC11244801 DOI: 10.1371/journal.pone.0306602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
The insectivorous Northern Pitcher Plant, Sarracenia purpurea, recruits a dynamic biotic community in the rainwater collected by its pitcher-shaped leaves. Insect capture and degradation within the pitcher fluid (phytotelma) has been well documented as a mechanism for supplementing the plant's nitrogen, phosphorous, and micronutrient requirements. Metagenomic studies have shown a diverse microbiome in this phytotelm environment, including taxa that contribute metabolically to prey digestion. In this investigation, we used high-throughput 16S rDNA sequencing and bioinformatics to analyze the S. purpurea phytotelm bacteriome as it changes through the growing season (May-September) in plants from the north-central region of the species' native range. Additionally, we used molecular techniques to detect and quantify bacterial nitrogenase genes (nifH) in all phytotelm samples to explore the hypothesis that diazotrophy is an additional mechanism of supplying biologically available nitrogen to S. purpurea. The results of this study indicate that while prokaryote diversity remains relatively stable in plants at different locations within our region, diversity changes significantly as the growing season progresses. Furthermore, nifH genes were detected at biologically significant concentrations in one hundred percent of samples, suggesting that nitrogen fixation may be an important contributor to the S. purpurea nutrient budget.
Collapse
Affiliation(s)
- Paul P. Melchior
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
- Department of Marine Science, Atlantic Technological University, Galway, Republic of Ireland
- Department of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Emma Reiss
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Zachary Payne
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Nhi Vuong
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Kari Hovorka
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Hunter L. Lindsay
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Gerardo R. Diaz
- Department of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Tara Gaire
- Department of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Noelle Noyes
- Department of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| |
Collapse
|
5
|
Morrison ML, Xue KS, Rosenberg NA. Quantifying compositional variability in microbial communities with FAVA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601929. [PMID: 39005283 PMCID: PMC11244974 DOI: 10.1101/2024.07.03.601929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Microbial communities vary across space, time, and individual hosts, presenting new challenges for the development of statistics measuring the variability of community composition. To understand differences across microbiome samples from different host individuals, sampling times, spatial locations, or experimental replicates, we present FAVA, a new normalized measure for characterizing compositional variability across multiple microbiome samples. FAVA quantifies variability across many samples of taxonomic or functional relative abundances in a single index ranging between 0 and 1, equaling 0 when all samples are identical and equaling 1 when each sample is entirely comprised of a single taxon. Its definition relies on the population-genetic statisticF S T , with samples playing the role of "populations" and taxa playing the role of "alleles." Its convenient mathematical properties allow users to compare disparate data sets. For example, FAVA values are commensurable across different numbers of taxonomic categories and different numbers of samples considered. We introduce extensions that incorporate phylogenetic similarity among taxa and spatial or temporal distances between samples. We illustrate how FAVA can be used to describe across-individual taxonomic variability in ruminant microbiomes at different regions along the gastrointestinal tract. In a second example, a longitudinal analysis of gut microbiomes of healthy human adults taking an antibiotic, we use FAVA to quantify the increase in temporal variability of microbiomes following the antibiotic course and to measure the duration of the antibiotic's influence on microbial variability. We have implemented this tool in an R package, FAVA, which can fit easily into existing pipelines for the analysis of microbial relative abundances.
Collapse
Affiliation(s)
| | - Katherine S. Xue
- Department of Biology, Stanford University, Stanford, CA 94305 USA
| | | |
Collapse
|
6
|
Li DD, Wang J, Jiang Y, Zhang P, Liu Y, Li YZ, Zhang Z. Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities. MICROBIOME 2024; 12:120. [PMID: 38956705 PMCID: PMC11218364 DOI: 10.1186/s40168-024-01838-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.
Collapse
Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
7
|
Isaac A, Mohamed AR, Amin SA. Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis. Appl Environ Microbiol 2024; 90:e0057024. [PMID: 38809046 PMCID: PMC11218658 DOI: 10.1128/aem.00570-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 05/30/2024] Open
Abstract
The complex interactions between bacterioplankton and phytoplankton have prompted numerous studies that investigate phytoplankton microbiomes with the aim of characterizing beneficial or opportunistic taxa and elucidating core bacterial members. Oftentimes, this knowledge is garnered through 16S rRNA gene profiling of microbiomes from phytoplankton isolated across spatial and temporal scales, yet these studies do not offer insight into microbiome assembly and structuring. In this study, we aimed to identify taxa central to structuring and establishing the microbiome of the ubiquitous diatom Asterionellopsis glacialis. We introduced a diverse environmental bacterial community to A. glacialis in nutrient-rich or nutrient-poor media in a continuous dilution culture setup and profiled the bacterial community over 7 days. 16S rRNA amplicon sequencing showed that cyanobacteria (Coleofasciculaceae) and Rhodobacteraceae dominate the microbiome early on and maintain a persistent association throughout the experiment. Differential abundance, co-abundance networks, and differential association analyses revealed that specific members of the family Rhodobacteraceae, particularly Sulfitobacter amplicon sequence variants, become integral members in microbiome assembly. In the presence of the diatom, Sulfitobacter species and other Rhodobacteraceae developed positive associations with taxa that are typically in high abundance in marine ecosystems (Pelagibacter and Synechococcus), leading to restructuring of the microbiome compared to diatom-free controls. These positive associations developed predominantly under oligotrophic conditions, highlighting the importance of investigating phytoplankton microbiomes in as close to natural conditions as possible to avoid biases that develop under routine laboratory conditions. These findings offer further insight into phytoplankton-bacteria interactions and illustrate the importance of Rhodobacteraceae, not merely as phytoplankton symbionts but as key taxa involved in microbiome assembly. IMPORTANCE Most, if not all, microeukaryotic organisms harbor an associated microbial community, termed the microbiome. The microscale interactions that occur between these partners have global-scale consequences, influencing marine primary productivity, carbon cycling, and harmful algal blooms to name but a few. Over the last decade, there has been a growing interest in the study of phytoplankton microbiomes, particularly within the context of bloom dynamics. However, long-standing questions remain regarding the process of phytoplankton microbiome assembly. The significance of our research is to tease apart the mechanism of microbiome assembly with a particular focus on identifying bacterial taxa, which may not merely be symbionts but architects of the phytoplankton microbiome. Our results strengthen the understanding of the ecological mechanisms that underpin phytoplankton-bacteria interactions in order to accurately predict marine ecosystem responses to environmental perturbations.
Collapse
Affiliation(s)
- Ashley Isaac
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Amin R. Mohamed
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Shady A. Amin
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Mubadala ACCESS Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| |
Collapse
|
8
|
Supty MSA, Jahan K, Lee JS, Choi KH. Epiphytic Bacterial Community Analysis of Ulva prolifera in Garorim and Muan Bays, Republic of Korea. Microorganisms 2024; 12:1142. [PMID: 38930524 PMCID: PMC11205692 DOI: 10.3390/microorganisms12061142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/16/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024] Open
Abstract
The bacterial communities related to seaweed can vary considerably across different locations, and these variations influence the seaweed's nutrition, growth, and development. To study this further, we evaluated the bacteria found on the green marine seaweed Ulva prolifera from Garorim Bay and Muan Bay, two key locations on Republic of Korea's west coast. Our analysis found notable differences in the bacterial communities between the two locations. Garorim Bay hosted a more diverse bacterial population, with the highest number of ASVs (871) compared to Muan Bay's 156 ASVs. In Muan Bay, more than 50% of the bacterial community was dominated by Pseudomonadota. On the other hand, Garorim Bay had a more balanced distribution between Bacteroidota and Pseudomonadota (37% and 35.5%, respectively). Additionally, Cyanobacteria, particularly Cyanothece aeruginosa, were found in significant numbers in Garorim Bay, making up 8% of the community. Mineral analysis indicated that Garorim Bay had higher levels of S, Na, Mg, Ca, and Fe. Function-wise, both locations exhibited bacterial enrichment in amino acid production, nucleosides, and nucleotide pathways. In conclusion, this study broadens our understanding of the bacterial communities associated with Ulva prolifera in Korean waters and provides a foundation for future research on the relationships between U. prolifera and its bacteria.
Collapse
Affiliation(s)
| | | | | | - Keun-Hyung Choi
- Department of Earth, Environmental and Space Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| |
Collapse
|
9
|
Chi Z, Li Y, Zhang J, Hu M, Wu Y, Fan X, Li Z, Miao Q, Li W. Effects of nitrogen application on ammonium assimilation and microenvironment in the rhizosphere of drip-irrigated sunflower under plastic mulch. Front Microbiol 2024; 15:1390331. [PMID: 38841064 PMCID: PMC11150556 DOI: 10.3389/fmicb.2024.1390331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
This study investigated the effect of nitrogen application on the rhizosphere soil microenvironment of sunflower and clarified the relationship between ammonium assimilation and the microenvironment. In a field experiment high (HN, 190 kg/hm2), medium (MN, 120 kg/hm2) and low nitrogen (CK, 50 kg/hm2) treatments were made to replicate plots of sunflowers using drip irrigation. Metagenomic sequencing was used to analyze the community structure and functional genes involved in the ammonium assimilation pathway in rhizosphere soil. The findings indicated that glnA and gltB played a crucial role in the ammonium assimilation pathway in sunflower rhizosphere soil, with Actinobacteria and Proteobacteria being the primary contributors. Compared with CK treatment, the relative abundance of Actinobacteria increased by 15.57% under MN treatment, while the relative abundance decreased at flowering and maturation stages. Conversely, the relative abundance of Proteobacteria was 28.57 and 61.26% higher in the MN treatment during anthesis and maturation period, respectively, compared with the CK. Furthermore, during the bud stage and anthesis, the abundance of Actinobacteria, Proteobacteria, and their dominant species were influenced mainly by rhizosphere soil EC, ammonium nitrogen (NH 4 + -N), and nitrate nitrogen (NO 3 - -N), whereas, at maturity, soil pH and NO 3 - -N played a more significant role in shaping the community of ammonium-assimilating microorganisms. The MN treatment increased the root length density, surface area density, and root volume density of sunflower at the bud, flowering, and maturity stages compared to the CK. Moreover, root exudates such as oxalate and malate were positively correlated with the dominant species of Actinobacteria and Proteobacteria during anthesis and the maturation period. Under drip irrigation, applying 120 kg/hm2 of nitrogen to sunflowers effectively promoted the community structure of ammonium-assimilating microorganisms in rhizosphere soil and had a positive influence on the rhizosphere soil microenvironment and sunflower root growth.
Collapse
Affiliation(s)
- Zhaonan Chi
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuxin Li
- Inner Mongolia Key Lab of Molecular Biology, Inner Mongolia Medical University, Hohhot, China
| | - Jiapeng Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Min Hu
- Vocational and Technical College of Inner Mongolia Agricultural University, Baotou, China
| | - Yixuan Wu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xueqin Fan
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhen Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Qingfeng Miao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Weiping Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| |
Collapse
|
10
|
Zhang L, Yuan L, Wen Y, Zhang M, Huang S, Wang S, Zhao Y, Hao X, Li L, Gao Q, Wang Y, Zhang S, Huang S, Liu K, Yu X, Li D, Xu J, Zhao B, Zhang L, Zhang H, Zhou W, Ai C. Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices. THE NEW PHYTOLOGIST 2024; 242:1275-1288. [PMID: 38426620 DOI: 10.1111/nph.19653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.
Collapse
Affiliation(s)
- Liyu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Liang Yuan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yanchen Wen
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Meiling Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Shuyu Huang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Shiyu Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yuanzheng Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Xiangxiang Hao
- Hailun National Observation and Research Station of Agroecosystems, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Lujun Li
- Hailun National Observation and Research Station of Agroecosystems, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Qiang Gao
- Jilin Agricultural University, Changchun, 130118, China
| | - Yin Wang
- Jilin Agricultural University, Changchun, 130118, China
| | - Shuiqing Zhang
- Institute of Plant Nutrition, Resource and Environment, Henan Academy of Agricultural Sciences, 116 Garden Road, Zhengzhou, 450002, China
| | - Shaomin Huang
- Institute of Plant Nutrition, Resource and Environment, Henan Academy of Agricultural Sciences, 116 Garden Road, Zhengzhou, 450002, China
| | - Kailou Liu
- Jiangxi Institute of Red Soil, National Engineering and Technology Research Center for Red Soil Improvement, Nanchang, 330046, China
| | - Xichu Yu
- Jiangxi Institute of Red Soil, National Engineering and Technology Research Center for Red Soil Improvement, Nanchang, 330046, China
| | - Dongchu Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiukai Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Bingqiang Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Lu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huimin Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Chao Ai
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| |
Collapse
|
11
|
Wang T, Weiss A, You L. A generic approach to infer community-level fitness of microbial genes. Proc Natl Acad Sci U S A 2024; 121:e2318380121. [PMID: 38635629 PMCID: PMC11047084 DOI: 10.1073/pnas.2318380121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the community-wide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment-function interplay of natural microbiomes.
Collapse
Affiliation(s)
- Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC27705
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, NC27705
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC27705
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Center for Quantitative Biodesign, Duke University, Durham, NC27705
| |
Collapse
|
12
|
Segaran TC, Azra MN, Mohd Noor MI, Danish-Daniel M, Burlakovs J, Lananan F, Xu J, Kari ZA, Wei LS. Knowledge mapping analysis of the global seaweed research using CiteSpace. Heliyon 2024; 10:e28418. [PMID: 38560172 PMCID: PMC10981124 DOI: 10.1016/j.heliyon.2024.e28418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/10/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Seaweed research has gained substantial momentum in recent years, attracting the attention of researchers, academic institutions, industries, policymakers, and philanthropists to explore its potential applications and benefits. Despite the growing body of literature, there is a paucity of comprehensive scientometric analyses, highlighting the need for an in-depth investigation. In this study, we utilized CiteSpace to examine the global seaweed research landscape through the Web of Science Core Collection database, assessing publication trends, collaboration patterns, network structures, and co-citation analyses across 48,278 original works published since 1975. Our results demonstrate a diverse and active research community, with a multitude of authors and journals contributing to the advancement of seaweed science. Thematic co-citation cluster analysis identified three primary research areas: "Coral reef," "Solar radiation," and "Mycosporine-like amino acid," emphasizing the multidisciplinary nature of seaweed research. The increasing prominence of "Chemical composition" and "Antioxidant" keywords indicates a burgeoning interest in characterizing the nutritional value and health-promoting properties of seaweed. Timeline co-citation analysis unveils that recent research priorities have emerged around the themes of coral reefs, ocean acidification, and antioxidants, underlining the evolving focus and interdisciplinary approach of the field. Moreover, our analysis highlights the potential of seaweed as a functional food product, poised to contribute significantly to addressing global food security and sustainability challenges. This study underscores the importance of bibliometric analysis in elucidating the global seaweed research landscape and emphasizes the need for sustained knowledge exchange and collaboration to drive the field forward. By revealing key findings and emerging trends, our research offers valuable insights for academics and stakeholders, fostering a more profound understanding of seaweed's potential and informing future research endeavors in this promising domain.
Collapse
Affiliation(s)
- Thirukanthan Chandra Segaran
- Institute of Climate Adaptation and Marine Biotechnology (ICAMB), Universiti Malaysia Terengganu (UMT), Kuala Nerus, 21030, Terengganu, Malaysia
| | - Mohamad Nor Azra
- Institute of Climate Adaptation and Marine Biotechnology (ICAMB), Universiti Malaysia Terengganu (UMT), Kuala Nerus, 21030, Terengganu, Malaysia
- Research Center for Marine and Land Bioindustry, Earth Sciences and Maritime Organization, National Research and Innovation Agency (BRIN), Pemenang, 83352, Indonesia
| | - Mohd Iqbal Mohd Noor
- Faculty of Business Management, Universiti Teknologi MARA (UiTM) (Pahang), 27600, Raub, Pahang, Malaysia
- Institute for Biodiversity and Sustainable Development, Universiti Teknologi MARA (UiTM), 40450, Shah Alam, Selangor, Malaysia
| | - Muhd Danish-Daniel
- Institute of Climate Adaptation and Marine Biotechnology (ICAMB), Universiti Malaysia Terengganu (UMT), Kuala Nerus, 21030, Terengganu, Malaysia
| | - Juris Burlakovs
- Mineral and Energy Economy Research Institute of the Polish Academy of Sciences, Poland
| | - Fathurrahman Lananan
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200 Besut, Terengganu, 21300, Malaysia
| | - Juntian Xu
- School of Marine Science and Fisheries, Jiangsu Ocean University, No. 59 Cangwu Road, Haizhou District, Lianyungang City, Jiangsu, China
| | - Zulhisyam Abdul Kari
- Department of Agricultural Science, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, 17600, Jeli, Kelantan, Malaysia
| | - Lee Seong Wei
- Department of Agricultural Science, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, 17600, Jeli, Kelantan, Malaysia
- Tropical Rainforest Research Centre (TRaCe), Universiti Malaysia Kelantan, Pulau Banding, 33300, Gerik, Perak, Malaysia
| |
Collapse
|
13
|
Zhao X, Wang J, Liu Q, Du W, Yang S, Cai P, Ni J. Multifunctionality promotes the prosperity of riverine planktonic diatoms in plateau. ENVIRONMENTAL RESEARCH 2024; 246:118148. [PMID: 38191040 DOI: 10.1016/j.envres.2024.118148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
Interpreting the biogeographic distribution and underlying mechanisms of functional traits not only contributes to revealing the spatiotemporal dynamics of species biodiversity but also helps to maintain ecological stability during environmental variations. However, little is known about the functional profiles of diatom communities over large river systems. Herein, we provided the first blueprints about the spatiotemporal distributions and driving forces of functional traits for both planktonic and sedimentary diatoms over the 6030 km continuum of the Yangtze River, with the help of the high-throughput sequencing and functional identification. By investigating the 28 functional traits affiliated into five categories, we found that planktonic diatom functions showed clearer landform-heterogeneity patterns (ANOSIM R = 0.336) than sedimentary functions (ANOSIM R = 0.172) along the river, represented by life-forms and ecological-guilds prominent in water-plateau as well as cell-sizes and life-forms particularly in sediment-plateau. Planktonic diatom functions also displayed higher richness and network complexity in plateau (richness: 58.70 ± 9.30, network edges: 65) than in non-plateau regions (23.82 ± 13.16, 16), promoting the stability and robustness of diatom functions against the high-radiation and low-temperature plateau environment. Environmental selection (mainly exerted by PAR, UV, and Tw) played crucial roles in determining the functional variations of planktonic diatoms (explaining 80.5%) rather than sedimentary diatoms (14.5%) between plateau and non-plateau regions. Meanwhile, planktonic diatom traits within life-forms were identified to be well responsive to the ecological environment quality (r = 0.56-0.60, P < 0.001) in the Yangtze. This study provided comprehensive insights into the multifunctionality of diatoms and their responses to environmental disturbance and environment quality, which helps to develop effective strategies for maintaining ecological stability in changing river environments.
Collapse
Affiliation(s)
- Xiaohui Zhao
- School of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an, 710048, PR China
| | - Jiawen Wang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China.
| | - Qingxiang Liu
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| | - Wenran Du
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| | - Pinggui Cai
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| |
Collapse
|
14
|
Lavecchia A, Fosso B, Engelen AH, Borin S, Manzari C, Picardi E, Pesole G, Placido A. Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism. MICROBIOME 2024; 12:47. [PMID: 38454513 PMCID: PMC10919026 DOI: 10.1186/s40168-023-01740-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024]
Abstract
BACKGROUND Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules. RESULTS To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites. CONCLUSION The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.
Collapse
Affiliation(s)
- Anna Lavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Aschwin H Engelen
- Center of Marine Sciences (CCMar), University of Algarve, Campus Gambelas, Faro, 8005-139, Portugal
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy
| | - Antonio Placido
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy.
| |
Collapse
|
15
|
Pearman WS, Morales SE, Vaux F, Gemmell NJ, Fraser CI. Host population crashes disrupt the diversity of associated marine microbiomes. Environ Microbiol 2024; 26:e16611. [PMID: 38519875 DOI: 10.1111/1462-2920.16611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 03/01/2024] [Indexed: 03/25/2024]
Abstract
Host-associated microbial communities are shaped by myriad factors ranging from host conditions, environmental conditions and other microbes. Disentangling the ecological impact of each of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host population structure to assess the influence of population crashes on marine microbial ecosystems. A large (7.8 magnitude) earthquake in New Zealand in 2016 led to widespread coastal uplift of up to ~6 m, sufficient to locally extirpate some intertidal southern bull kelp populations. These uplifted populations are slowly recovering, but remain at much lower densities than at nearby, less-uplifted sites. By comparing the microbial communities of the hosts from disturbed and relatively undisturbed populations using 16S rRNA gene amplicon sequencing, we observed that disturbed host populations supported higher functional, taxonomic and phylogenetic microbial beta diversity than non-disturbed host populations. Our findings shed light on microbiome ecological assembly processes, particularly highlighting that large-scale disturbances that affect host populations can dramatically influence microbiome structure. We suggest that disturbance-induced changes in host density limit the dispersal opportunities of microbes, with host community connectivity declining with the density of host populations.
Collapse
Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, Dunedin, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- National Institute of Water and Atmospheric Research Ltd, Auckland, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Felix Vaux
- National Institute of Water and Atmospheric Research Ltd, Auckland, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| |
Collapse
|
16
|
Freddi S, Rajabal V, Tetu SG, Gillings MR, Penesyan A. Microbial biofilms on macroalgae harbour diverse integron gene cassettes. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001446. [PMID: 38488860 PMCID: PMC10963911 DOI: 10.1099/mic.0.001446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
Integrons are genetic platforms that capture, rearrange and express mobile modules called gene cassettes. The best characterized gene cassettes encode antibiotic resistance, but the function of most integron gene cassettes remains unknown. Functional predictions suggest that many gene cassettes could encode proteins that facilitate interactions with other cells and with the extracellular environment. Because cell interactions are essential for biofilm stability, we sequenced gene cassettes from biofilms growing on the surface of the marine macroalgae Ulva australis and Sargassum linearifolium. Algal samples were obtained from coastal rock platforms around Sydney, Australia, using seawater as a control. We demonstrated that integrons in microbial biofilms did not sample genes randomly from the surrounding seawater, but harboured specific functions that potentially provided an adaptive advantage to both the bacterial cells in biofilm communities and their macroalgal host. Further, integron gene cassettes had a well-defined spatial distribution, suggesting that each bacterial biofilm acquired these genetic elements via sampling from a large but localized pool of gene cassettes. These findings suggest two forms of filtering: a selective acquisition of different integron-containing bacterial species into the distinct biofilms on Ulva and Sargassum surfaces, and a selective retention of unique populations of gene cassettes at each sampling location.
Collapse
Affiliation(s)
- Stefano Freddi
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, NSW 2109, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, NSW 2109, Australia
| | - Michael R. Gillings
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, NSW 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, NSW 2109, Australia
| |
Collapse
|
17
|
Liang X, Wan D, Tan L, Liu H. Dynamic changes of endophytic bacteria in the bark and leaves of medicinal plant Eucommia ulmoides in different seasons. Microbiol Res 2024; 280:127567. [PMID: 38103467 DOI: 10.1016/j.micres.2023.127567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
The bark and leaves of the Eucommia ulmoides Oliv. (E. ulmoides) have good medicinal value. Studies show endophytes play important roles in host medicinal plant secondary metabolite synthesis, with season being a key influencing factor. Therefore, we used 16 S rRNA to detect endophytic bacteria (EB) in E. ulmoides bark and leaves collected in winter, spring, summer, and autumn, and analyzed the contents of major active components respectively. The results showed that the species diversity and richness of EB of the E. ulmoides bark were higher than those of leaves in all seasons except fall. Among them, the higher species diversity and richness were found in the E. ulmoides bark in winter and spring. EB community structure differed significantly between medicinal tissues and seasons. Concurrently, the bark and leaves of E. ulmoides showed abundant characteristic EB across seasons. For active components, geniposidic acid showed a significant positive correlation with EB diversity and richness, while the opposite was true for aucubin. Additionally, some dominant EB exhibited close correlations with the accumulation of active components. Delftia, enriched in autumn, correlated significantly positively with aucubin. Notably, the impact of the same EB genera on active components differed across medicinal tissues. For example, Sphingomonas, enriched in summer, correlated significantly positively with pinoresinol diglucoside (PDG) in the bark, but with aucubin in the leaves. In summary, EB of E. ulmoides was demonstrated high seasonal dynamics and tissue specificity, with seasonal characteristic EB like Delftia and Sphingomonas correlating with the accumulation of active components in medicinal tissues.
Collapse
Affiliation(s)
- Xuejuan Liang
- Institute of Innovative Traditional Chinese Medications, Hunan Academy of Chinese Medicine, Changsha 410013, China
| | - Dan Wan
- Institute of Innovative Traditional Chinese Medications, Hunan Academy of Chinese Medicine, Changsha 410013, China
| | - Lei Tan
- Cili Meteorological Bureau, Zhangjiajie 410013, China
| | - Hao Liu
- Institute of Traditional Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha 410013, China.
| |
Collapse
|
18
|
LeBlanc NR, Harrigian FC. Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil. MICROBIAL ECOLOGY 2024; 87:44. [PMID: 38367043 PMCID: PMC10874327 DOI: 10.1007/s00248-024-02361-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.
Collapse
Affiliation(s)
- Nicholas R LeBlanc
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA.
| | - Fiona C Harrigian
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA
| |
Collapse
|
19
|
Rangel LI, Leveau JHJ. Applied microbiology of the phyllosphere. Appl Microbiol Biotechnol 2024; 108:211. [PMID: 38358509 PMCID: PMC10869387 DOI: 10.1007/s00253-024-13042-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.
Collapse
Affiliation(s)
- Lorena I Rangel
- Cell & Molecular Sciences, The James Hutton Institute, Dundee, Scotland, UK.
- Department of Plant Pathology, University of California, Davis, CA, USA.
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, CA, USA.
| |
Collapse
|
20
|
Taenzer L, Toth G, Hansel CM. Assessment of hydrogen peroxide as a bioindicator of stress in seaweed aquaculture. Sci Rep 2024; 14:1956. [PMID: 38263423 PMCID: PMC10806984 DOI: 10.1038/s41598-024-52182-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024] Open
Abstract
The rapid expansion in commercial seaweed farming has highlighted the need for more effective monitoring methods, and health diagnostics. The production of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) is a trait that is tied to all major macroalgal groups and holds significance both for its involvement in the oxidative stress response and in the production of climatically relevant gases such as halocarbons. Observations of increased production of H2O2 by plants as a stress response, along with its comparative stability and ease of quantification in seawater in comparison to other ROS, suggest that H2O2 could be used as an indicator of health. In this study we characterized aqueous H2O2 dynamics across a diel cycle, in response to small shifts in light and temperature, as well as when exposed to acute stress. Our results reveal that exposure to acute stressors leads to rapid and sustained concentrations of H2O2 that are orders of magnitude higher than changes in H2O2 concentrations observed throughout the day. These findings provide tantalizing evidence that monitoring H2O2 could be used as a health indicator in seaweed aquaculture and serve as an early warning sign of stress.
Collapse
Affiliation(s)
- Lina Taenzer
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Gunilla Toth
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
| |
Collapse
|
21
|
Díez-Vives C, Riesgo A. High compositional and functional similarity in the microbiome of deep-sea sponges. THE ISME JOURNAL 2024; 18:wrad030. [PMID: 38365260 PMCID: PMC10837836 DOI: 10.1093/ismejo/wrad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/18/2024]
Abstract
Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.
Collapse
Affiliation(s)
- Cristina Díez-Vives
- Department of Systems Biology, Centro Nacional de Biotecnología, c/ Darwin, 3, 28049 Madrid, Spain
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| |
Collapse
|
22
|
Khan T, Song W, Nappi J, Marzinelli EM, Egan S, Thomas T. Functional guilds and drivers of diversity in seaweed-associated bacteria. FEMS MICROBES 2023; 5:xtad023. [PMID: 38213395 PMCID: PMC10781435 DOI: 10.1093/femsmc/xtad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.
Collapse
Affiliation(s)
- Tahsin Khan
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Jadranka Nappi
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
23
|
Daybog I, Kolodny O. A computational framework for resolving the microbiome diversity conundrum. Nat Commun 2023; 14:7977. [PMID: 38042865 PMCID: PMC10693575 DOI: 10.1038/s41467-023-42768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 10/20/2023] [Indexed: 12/04/2023] Open
Abstract
Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
Collapse
Affiliation(s)
- Itay Daybog
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| |
Collapse
|
24
|
Kurokawa M, Higashi K, Yoshida K, Sato T, Maruyama S, Mori H, Kurokawa K. Metagenomic Thermometer. DNA Res 2023; 30:dsad024. [PMID: 37940329 PMCID: PMC10660216 DOI: 10.1093/dnares/dsad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/06/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
Various microorganisms exist in environments, and each of them has its optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, we developed a 'Metagenomic Thermometer' as a means of predicting environmental temperature based on metagenomic sequences. Temperature prediction of diverse environments using publicly available metagenomic data revealed that the Metagenomic Thermometer can predict environmental temperatures with small temperature changes and little influx of microorganisms from other environments. The accuracy of the Metagenomic Thermometer was also confirmed by a demonstration experiment using an artificial hot water canal. The Metagenomic Thermometer was also applied to human gut metagenomic samples, yielding a reasonably accurate value for human body temperature. The result further suggests that deep body temperature determines the dominant lineage of the gut community. Metagenomic Thermometer provides a new insight into temperature-driven community assembly based on amino-acid composition rather than microbial taxa.
Collapse
Affiliation(s)
- Masaomi Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Higashi
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Keisuke Yoshida
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Tomohiko Sato
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Shigenori Maruyama
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroshi Mori
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Genome Diversity Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Ken Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| |
Collapse
|
25
|
Zhou J, Qin W, Lu X, Yang Y, Stahl D, Jiao N, Zhou J, Liu J, Tu Q. The diversity and ecological significance of microbial traits potentially involved in B 12 biosynthesis in the global ocean. MLIFE 2023; 2:416-427. [PMID: 38818271 PMCID: PMC10989127 DOI: 10.1002/mlf2.12095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/21/2023] [Accepted: 10/04/2023] [Indexed: 06/01/2024]
Abstract
Cobalamin (B12), an essential nutrient and growth cofactor for many living organisms on Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related to B12 biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make-up of complex functional assemblages. By anchoring microbial traits potentially involved in B12 biosynthesis, we depict the biogeographic patterns of B12 biosynthesis genes and the taxa harboring them in the global ocean, despite the limitations of detecting de novo B12 synthesizers via metagenomes alone. Both the taxonomic and functional composition of B12 biosynthesis genes were strongly shaped by depth, differentiating the epipelagic zones from the mesopelagic layers. Functional genes related to B12 biosynthesis were relatively stably distributed across different oceans, but the taxa harboring them varied considerably, showing clear functional redundancy among microbial systems. Microbial taxa carrying B12 biosynthesis genes in the surface water were influenced by environmental factors such as temperature, oxygen, and nitrate. However, the composition of functional genes was only weakly associated with these environmental factors. Null model analyses demonstrated that determinism governed the variations in B12 biosynthesis genes, whereas a higher degree of stochasticity was associated with taxonomic variations. Significant associations were observed between the chlorophyll a concentration and B12 biosynthesis, confirming its importance in primary production in the global ocean. The results of this study reveal an essential ecological mechanism governing the assembly of microbes in nature: the environment selects for function rather than taxonomy; functional redundancy underlies stochastic community assembly.
Collapse
Affiliation(s)
- Jiayin Zhou
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
| | - Wei Qin
- School of Biological SciencesUniversity of OklahomaNormanOklahomaUSA
| | - Xinda Lu
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
DermBiont Inc.BostonMassachusettsUSA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - David Stahl
- Department of Civil and Environmental EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Nianzhi Jiao
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Institute of Marine Microbes and EcospheresXiamen UniversityXiamenChina
| | - Jizhong Zhou
- School of Biological SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Institute for Environmental Genomics, University of OklahomaNormanOklahomaUSA
- School of Civil Engineering and Environmental Sciences, University of OklahomaNormanOklahomaUSA
- School of Computer Sciences, University of OklahomaNormanOklahomaUSA
| | - Jihua Liu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
| | - Qichao Tu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
| |
Collapse
|
26
|
Pereira TJ, Walters TL, El-Shaffey HM, Bik HM, Frischer ME. The microbiome of the pelagic tunicate Dolioletta gegenbauri: A potential link between the grazing and microbial food web. Mol Ecol 2023; 32:6564-6579. [PMID: 35989550 DOI: 10.1111/mec.16668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022]
Abstract
Bloom-forming gelatinous zooplankton occur circumglobally and significantly influence the structure of pelagic marine food webs and biogeochemical cycling through interactions with microbial communities. During bloom conditions especially, gelatinous zooplankton are keystone taxa that help determine the fate of primary production, nutrient remineralization, and carbon export. Using the pelagic tunicate Dolioletta gegenbauri as a model system for gelatinous zooplankton, we carried out a laboratory-based feeding experiment to investigate the potential ecosystem impacts of doliolid gut microbiomes and microbial communities associated with doliolid faecal pellets and the surrounding seawater. Metabarcoding targeting Bacteria and Archaea 16S rRNA genes/Archaea) and qPCR approaches were used to characterize microbiome assemblages. Comparison between sample types revealed distinct patterns in microbial diversity and biomass that were replicable across experiments. These observations support the hypothesis that through their presence and trophic activity, doliolids influence the structure of pelagic food webs and biogeochemical cycling in subtropical continental shelf systems where tunicate blooms are common. Bacteria associated with starved doliolids (representative of the resident gut microbiome) possessed distinct low-biomass and low-diversity microbial assemblages, suggesting that the doliolid microbiome is optimized to support a detrital trophic mode. Bacterial genera Pseudoalteromomas and Shimia were the most abundant potential core microbiome taxa, similar to patterns observed in other marine invertebrates. Exploratory bioinformatic analyses of predicted functional genes suggest that doliolids, via their interactions with bacterial communities, may affect important biogeochemical processes including nitrogen, sulphur, and organic matter cycling.
Collapse
Affiliation(s)
- Tiago J Pereira
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Tina L Walters
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
| | - Hisham M El-Shaffey
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Holly M Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Marc E Frischer
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
| |
Collapse
|
27
|
Kost C, Patil KR, Friedman J, Garcia SL, Ralser M. Metabolic exchanges are ubiquitous in natural microbial communities. Nat Microbiol 2023; 8:2244-2252. [PMID: 37996708 DOI: 10.1038/s41564-023-01511-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 09/11/2023] [Indexed: 11/25/2023]
Abstract
Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.
Collapse
Affiliation(s)
- Christian Kost
- Osnabrück University, Department of Ecology, School of Biology/Chemistry, Osnabrück, Germany.
| | - Kiran Raosaheb Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany.
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| |
Collapse
|
28
|
Nappi J, Goncalves P, Khan T, Majzoub ME, Grobler AS, Marzinelli EM, Thomas T, Egan S. Differential priority effects impact taxonomy and functionality of host-associated microbiomes. Mol Ecol 2023; 32:6278-6293. [PMID: 34995388 DOI: 10.1111/mec.16336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 01/24/2023]
Abstract
Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.
Collapse
Affiliation(s)
- Jadranka Nappi
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Priscila Goncalves
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Tahsin Khan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Marwan E Majzoub
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Anna Sophia Grobler
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Ezequiel M Marzinelli
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Torsten Thomas
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
29
|
Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production. Microorganisms 2023; 11:2864. [PMID: 38138008 PMCID: PMC10745983 DOI: 10.3390/microorganisms11122864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.
Collapse
Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| |
Collapse
|
30
|
Song W, Li H, Zhou Y, Liu X, Li Y, Wang M, Li DD, Tu Q. Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms. Front Microbiol 2023; 14:1291242. [PMID: 38053549 PMCID: PMC10694361 DOI: 10.3389/fmicb.2023.1291242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.
Collapse
Affiliation(s)
- Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Dan-dan Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| |
Collapse
|
31
|
Trevelline BK, Sprockett D, DeLuca WV, Andreadis CR, Moeller AH, Tonra CM. Convergent remodelling of the gut microbiome is associated with host energetic condition over long-distance migration. Funct Ecol 2023; 37:2840-2854. [PMID: 38249446 PMCID: PMC10795773 DOI: 10.1111/1365-2435.14430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/25/2023] [Indexed: 01/23/2024]
Abstract
The gut microbiome can be thought of as a virtual organ given its immense metabolic capacity and profound effects on host physiology. Migratory birds are capable of adaptively modulating many aspects of their physiology to facilitate long-distance movements, raising the hypothesis that their microbiome may undergo a parallel remodeling process that helps to meet the energetic demands of migration.To test this hypothesis, we investigated changes in gut microbiome composition and function over the fall migration of the Blackpoll Warbler (Setophaga striata), which exhibits one of the longest known autumnal migratory routes of any songbird and rapidly undergoes extensive physiological remodeling during migration.Overall, our results showed that the Blackpoll Warbler microbiome differed significantly across phases of fall migration. This pattern was driven by a dramatic increase in the relative abundance of Proteobacteria, and more specifically a single 16S rRNA gene amplicon sequence variant belonging to the family Enterobacteriaceae. Further, Blackpoll Warblers exhibited a progressive reduction in microbiome diversity and within-group variance over migration, indicating convergence of microbiome composition among individuals during long-distance migration. Metagenomic analysis revealed that the gut microbiome of staging individuals was enriched in bacterial pathways involved in vitamin, amino acid, and fatty acid biosynthesis, as well as carbohydrate metabolism, and that these pathways were in turn positively associated with host body mass and subcutaneous fat deposits.Together, these results provide evidence that the gut microbiome of migratory birds may undergo adaptive remodeling to meet the physiological and energetic demands of long-distance migration.
Collapse
Affiliation(s)
- Brian K. Trevelline
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Daniel Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | | | - Catherine R. Andreadis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Department of Biological Sciences, University of Notre Dame, South Bend, IN, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Christopher M. Tonra
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
32
|
Liu J, Guo Y, Gu H, Liu Z, Hu X, Yu Z, Li Y, Li L, Sui Y, Jin J, Liu X, Adams JM, Wang G. Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes. THE ISME JOURNAL 2023; 17:1872-1883. [PMID: 37607984 PMCID: PMC10579271 DOI: 10.1038/s41396-023-01496-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
The microbiome function responses to land use change are important for the long-term prediction and management of soil ecological functions under human influence. However, it has remains uncertain how the biogeographic patterns of soil functional composition change when transitioning from natural steppe soils (NS) to agricultural soils (AS). We collected soil samples from adjacent pairs of AS and NS across 900 km of Mollisol areas in northeast China, and the soil functional composition was characterized using shotgun sequencing. AS had higher functional alpha-diversity indices with respect to KO trait richness and a higher Shannon index than NS. The distance-decay slopes of functional gene composition were steeper in AS than in NS along both spatial and environmental gradients. Land-use conversion from steppe to farmland diversified functional gene profiles both locally and spatially; it increased the abundances of functional genes related to labile carbon, but decreased those related to recalcitrant substrate mobilization (e.g., lignin), P cycling, and S cycling. The composition of gene functional traits was strongly driven by stochastic processes, while the degree of stochasticity was higher in NS than in AS, as revealed by the neutral community model and normalized stochasticity ratio analysis. Alpha-diversity of core functional genes was strongly related to multi-nutrient cycling in AS, suggesting a key relationship to soil fertility. The results of this study challenge the paradigm that the conversion of natural to agricultural habitat will homogenize soil properties and biology while reducing local and regional gene functional diversity.
Collapse
Affiliation(s)
- Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yaping Guo
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, P R China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Zhuxiu Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Lujun Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yueyu Sui
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Xiaobing Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, P R China.
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China.
| |
Collapse
|
33
|
Kuba GM, Spalding HL, Hill-Spanik KM, Williams TM, Paiano MO, Sherwood AR, Hauk BB, Kosaki RK, Fullerton H. Characterization of macroalgal-associated microbial communities from shallow to mesophotic depths at Manawai, Papahānaumokuākea Marine National Monument, Hawai'i. PeerJ 2023; 11:e16114. [PMID: 37842050 PMCID: PMC10569167 DOI: 10.7717/peerj.16114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/27/2023] [Indexed: 10/17/2023] Open
Abstract
The Papahānaumokuākea Marine National Monument, Hawai'i, is one of the most isolated and protected archipelagos in the world, making it a natural laboratory to examine macroalgal-microbial diversity because of limited direct anthropogenic impacts. We collected the most abundant macroalgae from nine sites ranging from shallow subtidal (1.5 m) to mesophotic (75 m) depths around Manawai (Pearl and Hermes Atoll). We characterized the macroalgal bacterial communities via high-throughput amplicon sequencing and compared the influence of host phylum, species, site, and depth on these relationships at a single atoll. Ochrophyta species had the lowest bacterial diversity compared to Chlorophyta and Rhodophyta. Site and/or depth may influence the microbial community structure associated with Microdictyon setchellianum, indicating a possible disconnect of these microbial communities among habitats. Chondria tumulosa, a cryptogenic species with invasive traits, differed in associated microbiota compared to the native Laurencia galtsoffii, an alga from the same family collected at the same site and depth. While there was overlap of bacterial communities across sites for some algal species, the majority had minimal macroalgal-microbial community connectivity across Manawai. This mesophotic system, therefore, did not appear to be refugia for shallow water coral reefs at microscopic scales. Additional studies are required to identify other significant influences on microbial community variation.
Collapse
Affiliation(s)
- Gabrielle M. Kuba
- Department of Biology, College of Charleston, Charleston, SC, United States
| | | | - Kristina M. Hill-Spanik
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
| | - Taylor M. Williams
- Department of Biology, College of Charleston, Charleston, SC, United States
| | - Monica O. Paiano
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Alison R. Sherwood
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Brian B. Hauk
- Cooperative Institute for Marine and Atmospheric Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
- Papahānaumokuākea Marine National Monument, National Oceanic and Atmospheric Administration, Honolulu, HI, United States
| | - Randall K. Kosaki
- Papahānaumokuākea Marine National Monument, National Oceanic and Atmospheric Administration, Honolulu, HI, United States
- Center for the Exploration of Coral Reef Ecosystems (XCoRE), Bishop Museum, Honolulu, HI, United States
| | - Heather Fullerton
- Department of Biology, College of Charleston, Charleston, SC, United States
| |
Collapse
|
34
|
Berdan EL, Roger F, Wellenreuther M, Kinnby A, Cervin G, Pereyra R, Töpel M, Johannesson K, Butlin RK, André C. A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea-Baltic Sea transition zone. Environ Microbiol 2023; 25:1659-1673. [PMID: 37032322 DOI: 10.1111/1462-2920.16379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/18/2023] [Indexed: 04/11/2023]
Abstract
Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about this community. Here, we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both microbiomes, but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea driven by changes in the frequency of different groups of known polysaccharide degraders. We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the different seaweed communities. Our results reveal the complexities of both the wrackbed microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.
Collapse
Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Fabian Roger
- Lund University, Centre for Environmental and Climate Science, Sölvegatan 37, 223 62, Lund, Sweden
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Alexandra Kinnby
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Gunnar Cervin
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Ricardo Pereyra
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Mats Töpel
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Roger K Butlin
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Carl André
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| |
Collapse
|
35
|
Vadillo Gonzalez S, Vranken S, Coleman MA, Wernberg T, Steinberg PD, Marzinelli EM. Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata. Mol Ecol 2023; 32:4584-4598. [PMID: 37332135 DOI: 10.1111/mec.17056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/21/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.
Collapse
Affiliation(s)
- Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
| | - Sofie Vranken
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
| | - Melinda A Coleman
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- New South Wales Fisheries, Department of Primary Industries, National Marine Science Centre, Coffs Harbour, New South Wales, Australia
| | - Thomas Wernberg
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- Institute of Marine Research, Floedevigen Research Station, His, Norway
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| |
Collapse
|
36
|
Blanchet S, Fargeot L, Raffard A. Phylogenetically-conserved candidate genes unify biodiversity-ecosystem function relationships and eco-evolutionary dynamics across biological scales. Mol Ecol 2023; 32:4467-4481. [PMID: 37296539 DOI: 10.1111/mec.17043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The intra- and interspecific facets of biodiversity have traditionally been analysed separately, limiting our understanding of how evolution has shaped biodiversity, how biodiversity (as a whole) alters ecological dynamics and hence eco-evolutionary feedbacks at the community scale. Here, we propose using candidate genes phylogenetically-conserved across species and sustaining functional traits as an inclusive biodiversity unit transcending the intra- and interspecific boundaries. This framework merges knowledge from functional genomics and functional ecology, and we first provide guidelines and a concrete example for identifying phylogenetically-conserved candidate genes (PCCGs) within communities and for measuring biodiversity from PCCGs. We then explain how biodiversity measured at PCCGs can be linked to ecosystem functions, which unifies recent observations that both intra- and interspecific biodiversity are important for ecosystem functions. We then highlight the eco-evolutionary processes shaping PCCG diversity patterns and argue that their respective role can be inferred from concepts derived from population genetics. Finally, we explain how PCCGs may shift the field of eco-evolutionary dynamics from a focal-species approach to a more realistic focal-community approach. This framework provides a novel perspective to investigate the global ecosystem consequences of diversity loss across biological scales, and how these ecological changes further alter biodiversity evolution.
Collapse
Affiliation(s)
- Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UAR2029, Moulis, France
| | - Laura Fargeot
- Centre National de la Recherche Scientifique (CNRS), Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UAR2029, Moulis, France
| | - Allan Raffard
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
| |
Collapse
|
37
|
Mateos K, Chappell G, Klos A, Le B, Boden J, Stüeken E, Anderson R. The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth. SCIENCE ADVANCES 2023; 9:eade4847. [PMID: 37418533 PMCID: PMC10328410 DOI: 10.1126/sciadv.ade4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/06/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earth's redox state, and affecting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. We use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the Mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth.
Collapse
Affiliation(s)
- Katherine Mateos
- Carleton College, Northfield, MN, USA
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Garrett Chappell
- Carleton College, Northfield, MN, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aya Klos
- Carleton College, Northfield, MN, USA
| | - Bryan Le
- Carleton College, Northfield, MN, USA
| | - Joanne Boden
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Eva Stüeken
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Rika Anderson
- Carleton College, Northfield, MN, USA
- NASA NExSS Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
| |
Collapse
|
38
|
Vale F, Sousa CA, Sousa H, Simões LC, McBain AJ, Simões M. Bacteria and microalgae associations in periphyton-mechanisms and biotechnological opportunities. FEMS Microbiol Rev 2023; 47:fuad047. [PMID: 37586879 DOI: 10.1093/femsre/fuad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
Phototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae-bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture, biorefinery, and wastewater bioremediation). In this review, we analyze the species dynamics (i.e. periphyton formation and factors determining the prevalence of one species over another), coexisting communities, exchange of resources, and communication mechanisms of periphytic microalgae and bacteria. We extend periphyton mathematical modelling as a tool to comprehend complex interactions. This review is expected to boost the applicability of microalgae-bacteria consortia, by drawing out knowledge from natural periphyton.
Collapse
Affiliation(s)
- Francisca Vale
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Cátia A Sousa
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Henrique Sousa
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Lúcia C Simões
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory in Biotechnology, Bioengineering and Microelectromechanical Systems, Braga/Guimarães, Portugal
| | - Andrew J McBain
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, United Kingdom
| | - Manuel Simões
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| |
Collapse
|
39
|
Fan D, Schwinghamer T, Liu S, Xia O, Ge C, Chen Q, Smith DL. Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes. FRONTIERS IN PLANT SCIENCE 2023; 14:1176648. [PMID: 37404529 PMCID: PMC10316030 DOI: 10.3389/fpls.2023.1176648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/24/2023] [Indexed: 07/06/2023]
Abstract
Introduction The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf). Methods In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes. Results and discussion Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.
Collapse
Affiliation(s)
- Di Fan
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Timothy Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shuaitong Liu
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Ouyuan Xia
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Chunmei Ge
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Qun Chen
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Donald L. Smith
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| |
Collapse
|
40
|
Parchemin C, Raviglione D, Mejait A, Sasal P, Faliex E, Clerissi C, Tapissier-Bontemps N. Antibacterial Activities and Life Cycle Stages of Asparagopsis armata: Implications of the Metabolome and Microbiome. Mar Drugs 2023; 21:363. [PMID: 37367688 DOI: 10.3390/md21060363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
The red alga Asparagopsis armata is a species with a haplodiplophasic life cycle alternating between morphologically distinct stages. The species is known for its various biological activities linked to the production of halogenated compounds, which are described as having several roles for the algae such as the control of epiphytic bacterial communities. Several studies have reported differences in targeted halogenated compounds (using gas chromatography-mass spectrometry analysis (GC-MS)) and antibacterial activities between the tetrasporophyte and the gametophyte stages. To enlarge this picture, we analysed the metabolome (using liquid chromatography-mass spectrometry (LC-MS)), the antibacterial activity and the bacterial communities associated with several stages of the life cycle of A. armata: gametophytes, tetrasporophytes and female gametophytes with developed cystocarps. Our results revealed that the relative abundance of several halogenated molecules including dibromoacetic acid and some more halogenated molecules fluctuated depending on the different stages of the algae. The antibacterial activity of the tetrasporophyte extract was significantly higher than that of the extracts of the other two stages. Several highly halogenated compounds, which discriminate algal stages, were identified as candidate molecules responsible for the observed variation in antibacterial activity. The tetrasporophyte also harboured a significantly higher specific bacterial diversity, which is associated with a different bacterial community composition than the other two stages. This study provides elements that could help in understanding the processes that take place throughout the life cycle of A. armata with different potential energy investments between the development of reproductive elements, the production of halogenated molecules and the dynamics of bacterial communities.
Collapse
Affiliation(s)
- Christelle Parchemin
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Delphine Raviglione
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Anouar Mejait
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Pierre Sasal
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Elisabeth Faliex
- Centre de Formation et de Recherche sur les Environnements Méditerranéens (CEFREM), UMR 5110 UPVD-CNRS, Université de Perpignan-Via Domitia, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Camille Clerissi
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Nathalie Tapissier-Bontemps
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| |
Collapse
|
41
|
Lu DC, Wang FQ, Amann RI, Teeling H, Du ZJ. Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae. MICROBIOME 2023; 11:126. [PMID: 37264413 PMCID: PMC10233909 DOI: 10.1186/s40168-023-01559-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species. RESULTS We sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera. CONCLUSIONS Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome. Video Abstract.
Collapse
Affiliation(s)
- De-Chen Lu
- Marine College, Shandong University, No. 180, Wenhua Xilu, Weihai, Shandong Province 264209 China
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Rudolf I. Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Zong-Jun Du
- Marine College, Shandong University, No. 180, Wenhua Xilu, Weihai, Shandong Province 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
| |
Collapse
|
42
|
Wang X, Han Q, Yu Q, Wang S, Yang J, Su W, Wan-Yan R, Sun X, Li H. Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil. ENVIRONMENTAL RESEARCH 2023; 225:115653. [PMID: 36898422 DOI: 10.1016/j.envres.2023.115653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.
Collapse
Affiliation(s)
- Xiaochen Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qian Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Sijie Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Ruijun Wan-Yan
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiaofang Sun
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
| |
Collapse
|
43
|
Sun S, Ma B, Wang G, Tan X. Linking microbial biogeochemical cycling genes to the rhizosphere of pioneering plants in a glacier foreland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:161944. [PMID: 36737018 DOI: 10.1016/j.scitotenv.2023.161944] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Glacier retreat raises global concerns but brings about the moment to study soil and ecosystem development. In nutrient-limited glacier forelands, the adaptability of pioneering plant and microbial species is facilitated by their interactions, including rhizosphere effects, but the details of this adaptability are not yet understood. In the rhizosphere of five pioneering plants, we comprehensively deciphered the microbial taxonomic and functional compositions. Two nitrogen-fixing microbial genera, Bradyrhizobium and Mesorhizobium, were among the most abundant taxa in the rhizomicrobiome. Moreover, several rhizobial genera, including Rhizobium, Pararhizobium, Allohrizobium, and Sinorhizobium, head the list of major modules in microbial co-occurrence networks, highlighting the vital roles of nitrogen-cycling taxa in the rhizomicrobiome of pioneering plants. Microbial genes involved in nitrogen, sulfur, phosphorus, and methane cycles were simultaneously correlated with microbial community dissimilarity, and 12 functional pathways were detected with distinct relative abundances among soils. Zooming in on the nitrogen-cycling genes, nifW, narC, nasA, nasB, and nirA were mainly responsible for the significant differences between soils. Furthermore, soil pH and the carbon/nitrogen ratio were among the topsoil properties interacting with nitrogen and sulfur cycling gene dissimilarity. These results explicitly linked biogeochemical cycling genes to the rhizomicrobiome and soil properties, revealing the roles of these genes as microbial drivers in mediating rhizosphere soil-plant-microbiome interactions.
Collapse
Affiliation(s)
- Shouqin Sun
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu 610065, China.
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Genxu Wang
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu 610065, China.
| | - Xiangfeng Tan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| |
Collapse
|
44
|
Cao J, Zhao P, Wang D, Zhao Y, Wang Z, Zhong N. Effects of a Nanonetwork-Structured Soil Conditioner on Microbial Community Structure. BIOLOGY 2023; 12:biology12050668. [PMID: 37237482 DOI: 10.3390/biology12050668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
Fertilizer application can increase yields, but nutrient runoff may cause environmental pollution and affect soil quality. A network-structured nanocomposite used as a soil conditioner is beneficial to crops and soil. However, the relationship between the soil conditioner and soil microbes is unclear. We evaluated the soil conditioner's impact on nutrient loss, pepper growth, soil improvement, and, especially, microbial community structure. High-throughput sequencing was applied to study the microbial communities. The microbial community structures of the soil conditioner treatment and the CK were significantly different, including in diversity and richness. The predominant bacterial phyla were Pseudomonadota, Actinomycetota, and Bacteroidota. Acidobacteriota and Chloroflexi were found in significantly higher numbers in the soil conditioner treatment. Ascomycota was the dominant fungal phylum. The Mortierellomycota phylum was found in significantly lower numbers in the CK. The bacteria and fungi at the genus level were positively correlated with the available K, available N, and pH, but were negatively correlated with the available P. Our results showed that the loss of nutrients controlled by the soil conditioner increased available N, which improved soil properties. Therefore, the microorganisms in the improved soil were changed. This study provides a correlation between improvements in microorganisms and the network-structured soil conditioner, which can promote plant growth and soil improvement.
Collapse
Affiliation(s)
- Jingjing Cao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Pan Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
| | - Dongfang Wang
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yonglong Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhiqin Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Naiqin Zhong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
| |
Collapse
|
45
|
Wang Q, Wang D, Agathokleous E, Cheng C, Shang B, Feng Z. Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone. Appl Environ Microbiol 2023; 89:e0018023. [PMID: 37022183 PMCID: PMC10132097 DOI: 10.1128/aem.00180-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/04/2023] [Indexed: 04/07/2023] Open
Abstract
Ethylenediurea (EDU) can effectively mitigate the crop yield loss caused by ozone (O3), a major, phytotoxic air pollutant. However, the relevant mechanisms are poorly understood, and the effect of EDU on soil ecosystems has not been comprehensively examined. In this study, a hybrid rice variety (Shenyou 63) was cultivated under ambient O3 and sprayed with 450 ppm EDU or water every 10 days. Real time quantitative polymerase chain reaction (RT-qPCR) showed that EDU had no significant effect on the microbial abundance in either rhizospheric or bulk soils. By applying both metagenomic sequencing and the direct assembly of nitrogen (N)-cycling genes, EDU was found to decrease the abundance of functional genes related to nitrification and denitrification processes. Moreover, EDU increased the abundance of genes involved in N-fixing. Although the abundance of some functional genes did not change significantly, nonmetric multidimensional scaling (NMDS) and a principal coordinates analysis (PCoA) suggested that the microbial community structure involved in N cycling was altered by EDU. The relative abundances of nifH-and norB-harboring microbial genera in the rhizosphere responded differently to EDU, suggesting the existence of functional redundancy, which may play a key role in sustaining microbially mediated N-cycling under ambient O3. IMPORTANCE Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. Due to its sensitivity to environmental changes, the microbial community can be used as an indicator to assess the environmental impacts of agricultural practices on soil quality. This study aimed to unravel the effects of EDU spray on the abundance, community structure, and ecological functions of microbial communities in the rhizosphere of rice plants. Our study provides a deep insight into the impact of EDU spray on microbial-mediated N cycling and the structure of N-cycling microbial communities. Our findings help to elucidate the mode of action of EDU in alleviating O3 stress in crops from the perspective of regulating the structure and function of the rhizospheric soil microbial community.
Collapse
Affiliation(s)
- Qi Wang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Dan Wang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Evgenios Agathokleous
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Cheng Cheng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Bo Shang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Zhaozhong Feng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| |
Collapse
|
46
|
Parizadeh M, Mimee B, Kembel SW. Soil microbial gene expression in an agricultural ecosystem varies with time and neonicotinoid seed treatments. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37083497 DOI: 10.1099/mic.0.001318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Neonicotinoids, a class of systemic insecticides, have been widely used for decades against various insect pests. Previous studies have reported non-target effects of neonicotinoids on some beneficial macro- and micro-organisms. Considering the crucial role the soil microbiota plays in sustaining soil fertility, it is critical to understand how neonicotinoid exposure affects the microbial taxonomic composition and gene expression. However, most studies to date have evaluated soil microbial taxonomic compositions or assessed microbial functions based on soil biochemical analysis. In this study, we have applied a metatranscriptomic approach to quantify the variability in soil microbial gene expression in a 2 year soybean/corn crop rotation in Quebec, Canada. We identified weak and temporally inconsistent effects of neonicotinoid application on soil microbial gene expression, as well as a strong temporal variation in soil microbial gene expression among months and years. Neonicotinoid seed treatment altered the expression of a small number of microbial genes, including genes associated with heat shock proteins, regulatory functions, metabolic processes and DNA repair. These changes in gene expression varied during the growing season and between years. Overall, the composition of soil microbial expressed genes seems to be more resilient and less affected by neonicotinoid application than soil microbial taxonomic composition. Our study is among the first to document the effects of neonicotinoid seed treatment on microbial gene expression and highlights the strong temporal variability of soil microbial gene expression and its responses to neonicotinoid seed treatments.
Collapse
Affiliation(s)
- Mona Parizadeh
- Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
- Département des Sciences Biologiques, Université du Québec à Montréal, 141 Avenue du Président-Kennedy, Montréal, Québec, H2X 1Y4, Canada
- Present address: Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Steven W Kembel
- Département des Sciences Biologiques, Université du Québec à Montréal, 141 Avenue du Président-Kennedy, Montréal, Québec, H2X 1Y4, Canada
| |
Collapse
|
47
|
Bhandari R, Sanz-Saez A, Leisner CP, Potnis N. Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere. ISME COMMUNICATIONS 2023; 3:24. [PMID: 36973329 PMCID: PMC10043289 DOI: 10.1038/s43705-023-00232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.
Collapse
Affiliation(s)
- Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Alvaro Sanz-Saez
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA.
| |
Collapse
|
48
|
Liu S, Gao J, Wang S, Li W, Wang A. Community differentiation of rhizosphere microorganisms and their responses to environmental factors at different development stages of medicinal plant Glehnia littoralis. PeerJ 2023; 11:e14988. [PMID: 36908810 PMCID: PMC9997192 DOI: 10.7717/peerj.14988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/12/2023] [Indexed: 03/08/2023] Open
Abstract
Rhizosphere microorganisms play a key role in affecting plant quality and productivity through its interaction with plant root system. To figure out the bottleneck of the decline of yield and quality in the traditional Chinese medicinal herbs Glehnia littoralis they now encounter, it is important to study the dynamics of rhizosphere microbiota during the cultivation of G. littoralis. In the present study, the composition, diversity and function of rhizosphere microbes at different development stages of G. littoralis, as well as the correlation between rhizosphere microbes and environmental factors were systematically studied by high-throughput sequencing. There were significant differences between the rhizosphere microbes at early and middle-late development stages. More beneficial bacteria, such as Proteobacteria, and more symbiotic and saprophytic fungi were observed at the middle-late development stage of G. littoralis, while beneficial bacteria such as Actinobacteria and polytrophic transitional fungi were abundant at all development stages. The results of redundancy analysis show that eight environmental factors drive the changes of microflora at different development stages. pH, soil organic matter (SOM) and available phosphorus (AP) had important positive effects on the bacterial and fungal communities at the early development stage; saccharase (SC) and nitrate nitrogen (NN) showed significant positive effects on the bacterial and fungal communities at the middle and late stages; while urease (UE), available potassium (AK), and alkaline phosphatase (AKP) have different effects on bacterial and fungal communities at different development stages. Random forest analysis identified 47 bacterial markers and 22 fungal markers that could be used to distinguish G. littoralis at different development stages. Network analysis showed that the rhizosphere microbes formed a complex mutualistic symbiosis network, which is beneficial to the growth and development of G. littoralis. These results suggest that host development stage and environmental factors have profound influence on the composition, diversity, community structure and function of plant rhizosphere microorganisms. This study provides a reference for optimizing the cultivation of G. littoralis.
Collapse
Affiliation(s)
- Shuliang Liu
- Ludong University, Yantai City, Shandong Province, China
| | - Jianxin Gao
- Ludong University, Yantai City, Shandong Province, China
| | - Shimeng Wang
- Ludong University, Yantai City, Shandong Province, China
| | - Weiwei Li
- Ludong University, Yantai City, Shandong Province, China
| | - Ailan Wang
- Ludong University, Yantai City, Shandong Province, China
| |
Collapse
|
49
|
Kardish MR, Stachowicz JJ. Local environment drives rapid shifts in composition and phylogenetic clustering of seagrass microbiomes. Sci Rep 2023; 13:3673. [PMID: 36871071 PMCID: PMC9985655 DOI: 10.1038/s41598-023-30194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Plant microbiomes depend on environmental conditions, stochasticity, host species, and genotype identity. Eelgrass (Zostera marina) is a unique system for plant-microbe interactions as a marine angiosperm growing in a physiologically-challenging environment with anoxic sediment, periodic exposure to air at low tide, and fluctuations in water clarity and flow. We tested the influence of host origin versus environment on eelgrass microbiome composition by transplanting 768 plants among four sites within Bodega Harbor, CA. Over three months following transplantation, we sampled microbial communities monthly on leaves and roots and sequenced the V4-V5 region of the 16S rRNA gene to assess community composition. The main driver of leaf and root microbiome composition was destination site; more modest effects of host origin site did not last longer than one month. Community phylogenetic analyses suggested that environmental filtering structures these communities, but the strength and nature of this filtering varies among sites and over time and roots and leaves show opposing gradients in clustering along a temperature gradient. We demonstrate that local environmental differences create rapid shifts in associated microbial community composition with potential functional implications for rapid host acclimation under shifting environmental conditions.
Collapse
Affiliation(s)
- Melissa R Kardish
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA, 95616, USA. .,Center for Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA.
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Center for Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| |
Collapse
|
50
|
Functional and Compositional Changes in the Fecal Microbiome of a Shorebird during Migratory Stopover. mSystems 2023; 8:e0112822. [PMID: 36786579 PMCID: PMC10134852 DOI: 10.1128/msystems.01128-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Shorebirds migrate long distances twice annually, which requires intense physiological and morphological adaptations, including the ability to rapidly gain weight via fat deposition at stopover locations. The role of the microbiome in weight gain in avian hosts is unresolved, but there is substantial evidence to support the hypothesis that the microbiome is involved with host weight from mammalian microbiome literature. Here, we collected 100 fecal samples of Ruddy Turnstones to investigate microbiome composition and function during stopover weight gain in Delaware Bay, USA. Using 16S rRNA sequencing on 90 of these samples and metatranscriptomic sequencing on 22, we show that taxonomic composition of the microbiome shifts during weight gain, as do functional aspects of the metatranscriptome. We identified 10 genes that are associated with weight class, and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds. IMPORTANCE Many animals migrate long distances annually, and these journeys require intense physiological and morphological adaptations. One such adaptation in shorebirds is the ability to rapidly gain weight at stopover locations in the middle of their migrations. The role of the microbiome in weight gain in birds is unresolved but is likely to play a role. Here, we collected 100 fecal samples from Ruddy Turnstones to investigate microbiome composition (who is there) and function (what they are doing) during stopover weight gain in Delaware Bay, USA. Using multiple molecular methods, we show that both taxonomic composition and function of the microbiome shifts during weight gain. We identified 10 genes that are associated with weight class, and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds.
Collapse
|