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Huang C, Xu Y, Zang R. Low functional redundancy revealed high vulnerability of the subtropical evergreen broadleaved forests to environmental change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173307. [PMID: 38777067 DOI: 10.1016/j.scitotenv.2024.173307] [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: 01/30/2024] [Revised: 04/21/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Anthropogenic-induced environmental changes threaten forest ecosystems by reducing their biodiversity and adaptive capacity. Understanding the sensitivity of ecosystem function to loss of diversity is vital in designing conservation strategies and maintaining the resilience of forest ecosystems in a changing world. Here, based on unique combinations of ten functional traits (termed as functional entities; FEs), we quantified the metrics of functional redundancy (FR) and functional vulnerability (FV) in 250 forest plots across five locations in subtropical evergreen broadleaved forests. We then examined the potential impacts of species loss on functional diversity in subtropical forest communities along environmental gradients (climate and soil). Results showed that the subtropical forests displayed a low level of functional redundancy (FR < 2). Over 75 % of the FEs in these subtropical forest communities were composed of only one species, with rare species emerging as pivotal contributors to these vulnerable FEs. The number of FEs and functional redundancy both increased with the rise in species richness, but functional vulnerability decreased with increasing species richness. Climatic factors, especially mean diurnal range, played crucial roles in determining the functions that the forest ecosystem delivers. Under variable temperature conditions, species in each plot were packed into a few FEs, leading to higher functional redundancy and lower functional vulnerability. These results highlighted that rare species contribute significantly to ecosystem functions and the highly diverse subtropical forest communities could show more insurance effects against species loss under stressful environmental conditions.
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Affiliation(s)
- Caishuang Huang
- School of Ecology and Environment, Southwest Forestry University, Kunming 650224, China
| | - Yue Xu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Runguo Zang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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Ahme A, Happe A, Striebel M, Cabrerizo MJ, Olsson M, Giesler J, Schulte-Hillen R, Sentimenti A, Kühne N, John U. Warming increases the compositional and functional variability of a temperate protist community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171971. [PMID: 38547992 DOI: 10.1016/j.scitotenv.2024.171971] [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: 02/02/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
Phototrophic protists are a fundamental component of the world's oceans by serving as the primary source of energy, oxygen, and organic nutrients for the entire ecosystem. Due to the high thermal seasonality of their habitat, temperate protists could harbour many well-adapted species that tolerate ocean warming. However, these species may not sustain ecosystem functions equally well. To address these uncertainties, we conducted a 30-day mesocosm experiment to investigate how moderate (12 °C) and substantial (18 °C) warming compared to ambient conditions (6 °C) affect the composition (18S rRNA metabarcoding) and ecosystem functions (biomass, gross oxygen productivity, nutritional quality - C:N and C:P ratio) of a North Sea spring bloom community. Our results revealed warming-driven shifts in dominant protist groups, with haptophytes thriving at 12 °C and diatoms at 18 °C. Species responses primarily depended on the species' thermal traits, with indirect temperature effects on grazing being less relevant and phosphorus acting as a critical modulator. The species Phaeocystis globosa showed highest biomass on low phosphate concentrations and relatively increased in some replicates of both warming treatments. In line with this, the C:P ratio varied more with the presence of P. globosa than with temperature. Examining further ecosystem responses under warming, our study revealed lowered gross oxygen productivity but increased biomass accumulation whereas the C:N ratio remained unaltered. Although North Sea species exhibited resilience to elevated temperatures, a diminished functional similarity and heightened compositional variability indicate potential ecosystem repercussions for higher trophic levels. In conclusion, our research stresses the multifaceted nature of temperature effects on protist communities, emphasising the need for a holistic understanding that encompasses trait-based responses, indirect effects, and functional dynamics in the face of exacerbating temperature changes.
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Affiliation(s)
- Antonia Ahme
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Anika Happe
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Maren Striebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Marco J Cabrerizo
- Department of Ecology, University of Granada, Campus Fuentenueva s/n 1, 18071 Granada, Spain; Department of Ecology and Animal Biology, University of Vigo, Campus Lagoas Marcosende s/n, 36310 Vigo, Spain
| | - Markus Olsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, 106 91 Stockholm, Sweden
| | - Jakob Giesler
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Ruben Schulte-Hillen
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79104 Freiburg i.Br., Germany
| | - Alexander Sentimenti
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79104 Freiburg i.Br., Germany
| | - Nancy Kühne
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Uwe John
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Ammerländer Heersstraße 231, 26129 Oldenburg, Germany
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Dekaj E, Gjini E. Pneumococcus and the stress-gradient hypothesis: A trade-off links R 0 and susceptibility to co-colonization across countries. Theor Popul Biol 2024; 156:77-92. [PMID: 38331222 DOI: 10.1016/j.tpb.2024.02.001] [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: 05/30/2022] [Revised: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Modern molecular technologies have revolutionized our understanding of bacterial epidemiology, but reported data across studies and different geographic endemic settings remain under-integrated in common theoretical frameworks. Pneumococcus serotype co-colonization, caused by the polymorphic bacteria Streptococcus pneumoniae, has been increasingly investigated and reported in recent years. While the global genomic diversity and serotype distribution of S. pneumoniae have been well-characterized, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of the bacteria. Gathering a rich dataset of cross-sectional pneumococcal colonization studies in the literature, we quantified patterns of transmission intensity and co-colonization prevalence variation in children populations across 17 geographic locations. Linking these data to an SIS model with cocolonization under the assumption of quasi-neutrality among multiple interacting strains, our analysis reveals strong patterns of negative co-variation between transmission intensity (R0) and susceptibility to co-colonization (k). In line with expectations from the stress-gradient-hypothesis in ecology (SGH), pneumococcus serotypes appear to compete more in co-colonization in high-transmission settings and compete less in low-transmission settings, a trade-off which ultimately leads to a conserved ratio of single to co-colonization μ=1/(R0-1)k. From the mathematical model's behavior, such conservation suggests preservation of 'stability-diversity-complexity' regimes in coexistence of similar co-colonizing strains. We find no major differences in serotype compositions across studies, pointing to adaptation of the same set of serotypes across variable environments as an explanation for their differential interaction in different transmission settings. Our work highlights that the understanding of transmission patterns of Streptococcus pneumoniae from global scale epidemiological data can benefit from simple analytical approaches that account for quasi-neutrality among strains, co-colonization, as well as variable environmental adaptation.
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Affiliation(s)
- Ermanda Dekaj
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Erida Gjini
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.
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Yan Y, Jarvie S, Zhang Q. Habitat loss weakens the positive relationship between grassland plant richness and above-ground biomass. eLife 2024; 12:RP91193. [PMID: 38497752 PMCID: PMC10948147 DOI: 10.7554/elife.91193] [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] [Indexed: 03/19/2024] Open
Abstract
Habitat loss and fragmentation per se have been shown to be a major threat to global biodiversity and ecosystem function. However, little is known about how habitat loss and fragmentation per se alters the relationship between biodiversity and ecosystem function (BEF relationship) in the natural landscape context. Based on 130 landscapes identified by a stratified random sampling in the agro-pastoral ecotone of northern China, we investigated the effects of landscape context (habitat loss and fragmentation per se) on plant richness, above-ground biomass, and the relationship between them in grassland communities using a structural equation model. We found that habitat loss directly decreased plant richness and hence decreased above-ground biomass, while fragmentation per se directly increased plant richness and hence increased above-ground biomass. Fragmentation per se also directly decreased soil water content and hence decreased above-ground biomass. Meanwhile, habitat loss decreased the magnitude of the positive relationship between plant richness and above-ground biomass by reducing the percentage of grassland specialists in the community, while fragmentation per se had no significant modulating effect on this relationship. These results demonstrate that habitat loss and fragmentation per se have inconsistent effects on BEF, with the BEF relationship being modulated by landscape context. Our findings emphasise that habitat loss rather than fragmentation per se can weaken the positive BEF relationship by decreasing the degree of habitat specialisation of the community.
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Affiliation(s)
- Yongzhi Yan
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia UniversityHohhotChina
| | | | - Qing Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia UniversityHohhotChina
- Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region)HohhotChina
- Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow RiverHohhotChina
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Amstutz A, Firth LB, Foggo A, Spicer JI, Hanley ME. The north-south divide? Macroalgal functional trait diversity and redundancy varies with intertidal aspect. ANNALS OF BOTANY 2024; 133:145-152. [PMID: 37971357 PMCID: PMC10921827 DOI: 10.1093/aob/mcad183] [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: 04/17/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND AIMS Marine macroalgae ('seaweeds') are critical to coastal ecosystem structure and function, but also vulnerable to the many environmental changes associated with anthropogenic climate change (ACC). The local habitat conditions underpinning observed and predicted ACC-driven changes in intertidal macroalgal communities are complex and probably site-specific and operate in addition to more commonly reported regional factors such as sea surface temperatures. METHODS We examined how the composition and functional trait expression of macroalgal communities in SW England varied with aspect (i.e. north-south orientation) at four sites with opposing Equator- (EF) and Pole-facing (PF) surfaces. Previous work at these sites had established that average annual (low tide) temperatures vary by 1.6 °C and that EF-surfaces experience six-fold more frequent extremes (i.e. >30 °C). KEY RESULTS PF macroalgal communities were consistently more taxon rich; 11 taxa were unique to PF habitats, with only one restricted to EF. Likewise, functional richness and dispersion were greater on PF-surfaces (dominated by algae with traits linked to rapid resource capture and utilization, but low desiccation tolerance), although differences in both taxon and functional richness were probably driven by the fact that less diverse EF-surfaces were dominated by desiccation-tolerant fucoids. CONCLUSIONS Although we cannot disentangle the influence of temperature variation on algal ecophysiology from the indirect effects of aspect on species interactions (niche pre-emption, competition, grazing, etc.), our study system provides an excellent model for understanding how environmental variation at local scales affects community composition and functioning. By virtue of enhanced taxonomic diversity, PF-aspects supported higher functional diversity and, consequently, greater effective functional redundancy. These differences may imbue PF-aspects with resilience against environmental perturbation, but if predicted increases in global temperatures are realized, some PF-sites may shift to a depauperate, desiccation-tolerant seaweed community with a concomitant loss of functional diversity and redundancy.
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Affiliation(s)
- Axelle Amstutz
- School of Biological and Marine Sciences, University of Plymouth, Drakes Circus, Plymouth, PL4 8AA, UK
| | - Louise B Firth
- School of Biological and Marine Sciences, University of Plymouth, Drakes Circus, Plymouth, PL4 8AA, UK
| | - Andy Foggo
- School of Biological and Marine Sciences, University of Plymouth, Drakes Circus, Plymouth, PL4 8AA, UK
| | - John I Spicer
- School of Biological and Marine Sciences, University of Plymouth, Drakes Circus, Plymouth, PL4 8AA, UK
| | - Mick E Hanley
- School of Biological and Marine Sciences, University of Plymouth, Drakes Circus, Plymouth, PL4 8AA, UK
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Seo DO, Holtzman DM. Current understanding of the Alzheimer's disease-associated microbiome and therapeutic strategies. Exp Mol Med 2024; 56:86-94. [PMID: 38172602 PMCID: PMC10834451 DOI: 10.1038/s12276-023-01146-2] [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: 08/19/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 01/05/2024] Open
Abstract
Alzheimer's disease (AD) is a fatal progressive neurodegenerative disease. Despite tremendous research efforts to understand this complex disease, the exact pathophysiology of the disease is not completely clear. Recently, anti-Aβ antibodies have been shown to remove amyloid from the brain and slow the clinical progression of mild dementia by ~30%. However, exploring alternative strategies is crucial to understanding and developing more effective therapeutic interventions. In recent years, the microbiota-gut-brain axis has received significant attention in the AD field. Numerous studies have suggested that alterations in the gut microbiota composition are associated with the progression of AD, and several underlying mechanisms have been proposed. However, studies in this area are still in their infancy, and many aspects of this field are just beginning to be explored and understood. Gaining a deeper understanding of the intricate interactions and signaling pathways involved in the microbiota-AD interaction is crucial for optimizing therapeutic strategies targeting gut microbiota to positively impact AD. In this review, we aim to summarize the current understanding of the microbiota-gut-brain axis in AD. We will discuss the existing evidence regarding the role of gut microbiota in AD pathogenesis, suggested underlying mechanisms, biological factors influencing the microbiome-gut-brain axis in AD, and remaining questions in the field. Last, we will discuss potential therapeutic approaches to recondition the community of gut microbiota to alleviate disease progression. An ongoing exploration of the gut-brain axis and the development of microbiota-based therapies hold the potential for advancing AD management in the future.
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Affiliation(s)
- Dong-Oh Seo
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - David M Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
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7
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Lei S, Wang X, Wang J, Zhang L, Liao L, Liu G, Wang G, Song Z, Zhang C. Effect of aridity on the β-diversity of alpine soil potential diazotrophs: insights into community assembly and co-occurrence patterns. mSystems 2024; 9:e0104223. [PMID: 38059620 PMCID: PMC10804954 DOI: 10.1128/msystems.01042-23] [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: 09/29/2023] [Accepted: 10/23/2023] [Indexed: 12/08/2023] Open
Abstract
Microbial diversity plays a vital role in the maintenance of ecosystem functions. However, the current understanding of mechanisms that shape microbial diversity along environmental gradients at broad spatial scales is relatively limited, especially for specific functional groups, such as potential diazotrophs. Here, we conducted an aridity-gradient transect survey from 60 sites across the Tibetan Plateau, the largest alpine ecosystem of the planet, to investigate the ecological processes (e.g., local species pools, community assembly processes, and co-occurrence patterns) that underlie the β-diversity of alpine soil potential diazotrophic communities. We found that aridity strongly and negatively affected the abundance, richness, and β-diversity of soil diazotrophs. Diazotrophs displayed a distance-decay pattern along the aridity gradient, with organisms living in lower aridity habitats having a stronger distance-decay pattern. Arid habitats had lower co-occurrence complexity, including the number of edges and vertices, the average degree, and the number of keystone taxa, as compared with humid habitats. Local species pools explained limited variations in potential diazotrophic β-diversity. In contrast, co-occurrence patterns and stochastic processes (e.g., dispersal limitation and ecological drift) played a significant role in regulating potential diazotrophic β-diversity. The relative importance of stochastic processes and co-occurrence patterns changed with increasing aridity, with stochastic processes weakening whereas that of co-occurrence patterns enhancing. The genera Geobacter and Paenibacillus were identified as keystone taxa of co-occurrence patterns that are associated with β-diversity. In summary, aridity affects the co-occurrence patterns and community assembly by regulating soil and vegetation characteristics and ultimately shapes the β-diversity of potential diazotrophs. These findings highlight the importance of co-occurrence patterns in structuring microbial diversity and advance the current understanding of mechanisms that drive belowground communities.IMPORTANCERecent studies have shown that community assembly processes and species pools are the main drivers of β-diversity in grassland microbial communities. However, co-occurrence patterns can also drive β-diversity formation by influencing the dispersal and migration of species, the importance of which has not been reported in previous studies. Assessing the impact of co-occurrence patterns on β-diversity is important for understanding the mechanisms of diversity formation. Our study highlights the influence of microbial co-occurrence patterns on β-diversity and combines the drivers of community β-diversity with drought variation, revealing that drought indirectly affects β-diversity by influencing diazotrophic co-occurrence patterns and community assembly.
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Affiliation(s)
- Shilong Lei
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangtao Wang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Jie Wang
- College of Forestry, Guizhou University, Guiyang, China
| | - Lu Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Lirong Liao
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guobin Liu
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoliang Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Science, Yangling, Shaanxi, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Zhang
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
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Yu XA, McLean C, Hehemann JH, Angeles-Albores D, Wu F, Muszyński A, Corzett CH, Azadi P, Kujawinski EB, Alm EJ, Polz MF. Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics. THE ISME JOURNAL 2024; 18:wrad013. [PMID: 38365244 PMCID: PMC10811730 DOI: 10.1093/ismejo/wrad013] [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: 10/31/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.
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Affiliation(s)
- Xiaoqian Annie Yu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Craig McLean
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Jan-Hendrik Hehemann
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David Angeles-Albores
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Eric J Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Martin F Polz
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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9
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Luo W, Wang Y, Cahill JF, Luan F, Zhong Y, Li Y, Li B, Chu C. Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest. Ecology 2024; 105:e4189. [PMID: 37877169 DOI: 10.1002/ecy.4189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/25/2023] [Indexed: 10/26/2023]
Abstract
Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains largely unknown. As β diversity can reflect the degree of community-wide biotic homogenization, such information is crucial for better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0-30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw ) and mean nearest neighbor distance (Dnn ) to quantify species ecological differences, we first tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.
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Affiliation(s)
- Wenqi Luo
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Youshi Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fucheng Luan
- Guangdong Chebaling National Nature Reserve, Shaoguan, China
| | - Yonglin Zhong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhi Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Buhang Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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10
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Gralka M. Searching for Principles of Microbial Ecology Across Levels of Biological Organization. Integr Comp Biol 2023; 63:1520-1531. [PMID: 37280177 PMCID: PMC10755194 DOI: 10.1093/icb/icad060] [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: 02/27/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities, is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems.
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Affiliation(s)
- Matti Gralka
- Systems Biology lab, Amsterdam Institute for Life and Environment (A-LIFE), Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV, The Netherlands
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11
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Schnyder E, Bodelier PLE, Hartmann M, Henneberger R, Niklaus PA. Experimental erosion of microbial diversity decreases soil CH 4 consumption rates. Ecology 2023; 104:e4178. [PMID: 37782571 DOI: 10.1002/ecy.4178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/11/2023] [Accepted: 08/25/2023] [Indexed: 10/04/2023]
Abstract
Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4 ) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 101 -107 -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.
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Affiliation(s)
- Elvira Schnyder
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martin Hartmann
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ruth Henneberger
- Institute of Molecular Health Science, ETH Zürich, Zürich, Switzerland
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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Morlino MS, Serna García R, Savio F, Zampieri G, Morosinotto T, Treu L, Campanaro S. Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches. Biotechnol Adv 2023; 69:108264. [PMID: 37775073 DOI: 10.1016/j.biotechadv.2023.108264] [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: 07/14/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO2 bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.
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Affiliation(s)
- Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Rebecca Serna García
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Filippo Savio
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
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Gómez-Varela D, Xian F, Grundtner S, Sondermann JR, Carta G, Schmidt M. Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics. Front Microbiol 2023; 14:1258703. [PMID: 37908546 PMCID: PMC10613666 DOI: 10.3389/fmicb.2023.1258703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction Metaproteomics is a rapidly advancing field that offers unique insights into the taxonomic composition and the functional activity of microbial communities, and their effects on host physiology. Classically, data-dependent acquisition (DDA) mass spectrometry (MS) has been applied for peptide identification and quantification in metaproteomics. However, DDA-MS exhibits well-known limitations in terms of depth, sensitivity, and reproducibility. Consequently, methodological improvements are required to better characterize the protein landscape of microbiomes and their interactions with the host. Methods We present an optimized proteomic workflow that utilizes the information captured by Parallel Accumulation-Serial Fragmentation (PASEF) MS for comprehensive metaproteomic studies in complex fecal samples of mice. Results and discussion We show that implementing PASEF using a DDA acquisition scheme (DDA-PASEF) increased peptide quantification up to 5 times and reached higher accuracy and reproducibility compared to previously published classical DDA and data-independent acquisition (DIA) methods. Furthermore, we demonstrate that the combination of DIA, PASEF, and neuronal-network-based data analysis, was superior to DDA-PASEF in all mentioned parameters. Importantly, DIA-PASEF expanded the dynamic range towards low-abundant proteins and it doubled the quantification of proteins with unknown or uncharacterized functions. Compared to previous classical DDA metaproteomic studies, DIA-PASEF resulted in the quantification of up to 4 times more taxonomic units using 16 times less injected peptides and 4 times shorter chromatography gradients. Moreover, 131 additional functional pathways distributed across more and even uniquely identified taxa were profiled as revealed by a peptide-centric taxonomic-functional analysis. We tested our workflow on a validated preclinical mouse model of neuropathic pain to assess longitudinal changes in host-gut microbiome interactions associated with pain - an unexplored topic for metaproteomics. We uncovered the significant enrichment of two bacterial classes upon pain, and, in addition, the upregulation of metabolic activities previously linked to chronic pain as well as various hitherto unknown ones. Furthermore, our data revealed pain-associated dynamics of proteome complexes implicated in the crosstalk between the host immune system and the gut microbiome. In conclusion, the DIA-PASEF metaproteomic workflow presented here provides a stepping stone towards a deeper understanding of microbial ecosystems across the breadth of biomedical and biotechnological fields.
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Ujaoney AK, Anaganti N, Padwal MK, Basu B. Deinococcus lineage and Rad52 family-related protein DR0041 is involved in DNA protection and compaction. Int J Biol Macromol 2023; 248:125885. [PMID: 37473881 DOI: 10.1016/j.ijbiomac.2023.125885] [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: 05/08/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
DR0041 ORF encodes an uncharacterized Deinococcus lineage protein. We earlier reported presence of DR0041 protein in DNA repair complexes of Ssb and RecA in Deinococcus radiodurans. Here, we systematically examined the role of DR0041 in DNA metabolism using various experimental methodologies including electrophoretic mobility assays, nuclease assays, strand exchange assays and transmission electron microscopy. Interaction between DR0041 and the C-terminal acidic tail of Ssb was assessed through co-expression and in vivo cross-linking studies. A knockout mutant was constructed to understand importance of DR0041 ORF for various physiological processes. Results highlight binding of DR0041 protein to single-stranded and double-stranded DNA, interaction with Ssb-coated single-stranded DNA without interference with RecA-mediated strand exchange, protection of DNA from exonucleases, and compaction of high molecular weight DNA molecules into tightly condensed forms. Bridging and compaction of sheared DNA by DR0041 protein might have implications in the preservation of damaged DNA templates to maintain genome integrity upon exposure to gamma irradiation. Our results suggest that DR0041 protein is dispensable for growth under standard growth conditions and following gamma irradiation but contributes to protection of DNA during transformation. We discuss the role of DR0041 protein from the perspective of protection of broken DNA templates and functional redundancy.
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Affiliation(s)
- Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Narasimha Anaganti
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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15
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White BE, Hovenden MJ, Barmuta LA. Multifunctional redundancy: Impossible or undetected? Ecol Evol 2023; 13:e10409. [PMID: 37593757 PMCID: PMC10427898 DOI: 10.1002/ece3.10409] [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: 07/10/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023] Open
Abstract
The diversity-functioning relationship is a pillar of ecology. Two significant concepts have emerged from this relationship: redundancy, the asymptotic relationship between diversity and functioning, and multifunctionality, a monotonic relationship between diversity and multiple functions occurring simultaneously. However, multifunctional redundancy, an asymptotic relationship between diversity and multiple functions occurring simultaneously, is rarely detected in research. Here we assess whether this lack of detection is due to its true rarity, or due to systematic research error. We discuss how inconsistencies in the use of terms such as 'function' lead to mismatched research. We consider the different techniques used to calculate multifunctionality and point out a rarely considered issue: how determining a function's maximum rate affects multifunctionality metrics. Lastly, we critique how a lack of consideration of multitrophic, spatiotemporal, interactions and community assembly processes in designed experiments significantly reduces the likelihood of detecting multifunctional redundancy. Multifunctionality research up to this stage has made significant contributions to our understanding of the diversity-functioning relationship, and we believe that multifunctional redundancy is detectable with the use of appropriate methodologies.
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Affiliation(s)
- Bridget E. White
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Mark J. Hovenden
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Leon A. Barmuta
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
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16
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Janowski D, Leski T. Landscape-scale mapping of soil fungal distribution: proposing a new NGS-based approach. Sci Rep 2023; 13:10280. [PMID: 37355666 PMCID: PMC10290699 DOI: 10.1038/s41598-023-37538-7] [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: 04/12/2023] [Accepted: 06/23/2023] [Indexed: 06/26/2023] Open
Abstract
Soil fungi play an indispensable role in the functioning of terrestrial habitats. Most landscape-scale studies of soil fungal diversity try to identify the fungal taxa present at a study site and define the relationships between their abundance and environmental factors. The specific spatial distribution of these fungi over the site, however, is not addressed. Our study's main objective is to propose a novel approach to landscape-scale mapping of soil fungi distribution using next generation sequencing and geographic information system applications. Furthermore, to test the proposed approach and discuss its performance, we aimed to conduct a case study mapping the spatial distribution of soil fungi on the Wielka Żuława island. The case study was performed on the Wielka Żuława island in northern Poland, where soil samples were collected every 100 m in an even grid. The fungal taxa and their relative abundance in each sample were assessed using the Illumina platform. Using the data obtained for the sampled points, maps of soil fungi spatial distribution were generated using three common interpolators: inverted distance weighted (IDW), B-spline, and ordinary Kriging. The proposed approach succeeded in creating maps of fungal distribution on Wielka Żuława. The most abundant groups of soil fungi were Penicillium on the genus level, Aspergillaceae on the family level, and ectomycorrhizal fungi on the trophic group level. Ordinary Kriging proved to be the most accurate at predicting relative abundance values for the groups of fungi significantly spatially autocorrelated at the sampled scale. For the groups of fungi not displaying spatial autocorrelation at the sampled scale, IDW provided the most accurate predictions of their relative abundance. Although less accurate at predicting exact relative abundance values, B-spline performed best in delineating the spatial patterns of soil fungi distribution. The proposed approach to landscape-scale mapping of soil fungi distribution could provide new insights into the ecology of soil fungi and terrestrial ecosystems in general. Producing maps of predicted fungal distribution in landscape-scale soil fungi diversity studies would also facilitate the reusability and replicability of the results. Outside the area of research, mapping the distribution of soil fungi could prove helpful in areas such as agriculture and forestry, nature conservation, and urban planning.
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Affiliation(s)
- Daniel Janowski
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland.
- Department of Natural Environmental Studies, The University of Tokyo, Kashiwa, Chiba, Japan.
| | - Tomasz Leski
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
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Khatib L, Subasi BS, Fishman B, Kapun M, Tauber E. Unveiling Subtle Geographical Clines: Phenotypic Effects and Dynamics of Circadian Clock Gene Polymorphisms. BIOLOGY 2023; 12:858. [PMID: 37372143 DOI: 10.3390/biology12060858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Our understanding of the gene regulatory network that constitutes the circadian clock has greatly increased in recent decades, notably due to the use of Drosophila as a model system. In contrast, the analysis of natural genetic variation that enables the robust function of the clock under a broad range of environments has developed more slowly. In the current study, we analyzed comprehensive genome sequencing data from wild European populations of Drosophila, which were densely sampled through time and space. We identified hundreds of single nucleotide polymorphisms (SNPs) in nine genes associated with the clock, 276 of which exhibited a latitudinal cline in their allele frequencies. While the effect sizes of these clinal patterns were small, indicating subtle adaptations driven by natural selection, they provided important insights into the genetic dynamics of circadian rhythms in natural populations. We selected nine SNPs in different genes and assessed their impact on circadian and seasonal phenotypes by reconstructing outbred populations fixed for either of the SNP alleles, from inbred DGRP strains. The circadian free-running period of the locomotor activity rhythm was affected by an SNP in doubletime (dbt) and eyes absent (Eya). The SNPs in Clock (Clk), Shaggy (Sgg), period (per), and timeless (tim) affected the acrophase. The alleles of the SNP in Eya conferred different levels of diapause and the chill coma recovery response.
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Affiliation(s)
- Loren Khatib
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Bengisu Sezen Subasi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Bettina Fishman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Martin Kapun
- Natural History Museum Vienna, 1010 Vienna, Austria
- Department of Cell and Developmental Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel
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18
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Wang Y, Zeng X, Zhang Y, Zhang N, Xu L, Wu C. Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil. J Environ Sci (China) 2023; 127:15-29. [PMID: 36522049 DOI: 10.1016/j.jes.2022.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/17/2023]
Abstract
Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.
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Affiliation(s)
- Yanan Wang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Xibai Zeng
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China.
| | - Yang Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Nan Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Liyang Xu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Cuixia Wu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
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Liu X, Nie Y, Wu XL. Predicting microbial community compositions in wastewater treatment plants using artificial neural networks. MICROBIOME 2023; 11:93. [PMID: 37106397 PMCID: PMC10142226 DOI: 10.1186/s40168-023-01519-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Activated sludge (AS) of wastewater treatment plants (WWTPs) is one of the world's largest artificial microbial ecosystems and the microbial community of the AS system is closely related to WWTPs' performance. However, how to predict its community structure is still unclear. RESULTS Here, we used artificial neural networks (ANN) to predict the microbial compositions of AS systems collected from WWTPs located worldwide. The predictive accuracy R21:1 of the Shannon-Wiener index reached 60.42%, and the average R21:1 of amplicon sequence variants (ASVs) appearing in at least 10% of samples and core taxa were 35.09% and 42.99%, respectively. We also found that the predictability of ASVs was significantly positively correlated with their relative abundance and occurrence frequency, but significantly negatively correlated with potential migration rate. The typical functional groups such as nitrifiers, denitrifiers, polyphosphate-accumulating organisms (PAOs), glycogen-accumulating organisms (GAOs), and filamentous organisms in AS systems could also be well recovered using ANN models, with R21:1 ranging from 32.62% to 56.81%. Furthermore, we found that whether industry wastewater source contained in inflow (IndConInf) had good predictive abilities, although its correlation with ASVs in the Mantel test analysis was weak, which suggested important factors that cannot be identified using traditional methods may be highlighted by the ANN model. CONCLUSIONS We demonstrated that the microbial compositions and major functional groups of AS systems are predictable using our approach, and IndConInf has a significant impact on the prediction. Our results provide a better understanding of the factors affecting AS communities through the prediction of the microbial community of AS systems, which could lead to insights for improved operating parameters and control of community structure. Video Abstract.
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Affiliation(s)
- Xiaonan Liu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, 100871, China.
- Institute of Ocean Research, Peking University, Beijing, 100871, China.
- Institute of Ecology, Peking University, Beijing, 100871, China.
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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.
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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
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Kalu EI, Reyes-Prieto A, Barbeau MA. Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy. ISME COMMUNICATIONS 2023; 3:21. [PMID: 36918616 PMCID: PMC10014957 DOI: 10.1038/s43705-023-00226-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.
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Affiliation(s)
- Eke I Kalu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada.
| | | | - Myriam A Barbeau
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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22
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Xing W, Gai X, Ju F, Chen G. Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160273. [PMID: 36460109 DOI: 10.1016/j.scitotenv.2022.160273] [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: 09/08/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16-31.05 % and 30.37-15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.
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Affiliation(s)
- Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China
| | - Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, PR China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China.
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23
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Zhang L, Liu X, Sun Z, Bu W, Bongers FJ, Song X, Yang J, Sun Z, Li Y, Li S, Cao M, Ma K, Swenson NG. Functional trait space and redundancy of plant communities decrease toward cold temperature at high altitudes in Southwest China. SCIENCE CHINA. LIFE SCIENCES 2023; 66:376-384. [PMID: 35876972 DOI: 10.1007/s11427-021-2135-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/31/2022] [Indexed: 12/01/2022]
Abstract
Plant communities in mountainous areas shift gradually as climatic conditions change with altitude. How trait structure in multivariate space adapts to these varying climates in natural forest stands is unclear. Studying the multivariate functional trait structure and redundancy of tree communities along altitude gradients is crucial to understanding how temperature change affects natural forest stands. In this study, the leaf area, specific leaf area, leaf carbon, nitrogen, and phosphorous content from 1,590 trees were collected and used to construct the functional trait space of 12 plant communities at altitudes ranging from 800 m to 3,800 m across three mountains. Hypervolume overlap was calculated to quantify species trait redundancy per community. First, hypervolumes of species exclusion and full species set were calculated, respectively. Second, the overlap between these two volumes was calculated to obtain hypervolume overlap. Results showed that the functional trait space significantly increased with mean annual temperature toward lower altitudes within and across three mountains, whereas species trait redundancy had different patterns between mountains. Thus, warming can widen functional trait space and alter the redundancy in plant communities. The inconsistent patterns of redundancy between mountains suggest that warming exerts varying influences on different ecosystems. Identification of climate-vulnerable ecosystems is important in the face of global warming.
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Affiliation(s)
- Lan Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaojuan Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhenhua Sun
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Wensheng Bu
- Key Laboratory of State Forestry Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Franca J Bongers
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaoyang Song
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Jie Yang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Zhenkai Sun
- Key Laboratory of Tree Breeding and Cultivation, Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yin Li
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, 365004, China
| | - Shan Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Min Cao
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Nathan G Swenson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556, USA
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24
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Qian F, Huang X, Bao Y. Heavy metals reshaping the structure and function of phylloplane bacterial community of native plant Tamarix ramosissima from Pb/Cd/Cu/Zn smelting regions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 251:114495. [PMID: 36640572 DOI: 10.1016/j.ecoenv.2022.114495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Heavy metal (HM) is noxious element that cannot be biodegraded, thus accumulating in the environment and posing a serious threat to the ecology. Plant phylloplane harbors diverse microbial communities that profoundly influence ecosystem functioning and host health. With more HM accumulating around smelters, native plants and microbes in various habitats tend to suffer from HM. However, the response of phylloplane bacteria of native plants to HM remains unclear. Thus, this study aimed to explain the response of Tamarix ramosissima, a phylloplane bacterial community to HM as well as the effect of the process on host growth in situ by investigating the potential source of HM and bacterial community shift. Results showed that, in most cases, the contaminated site with high HM level caused more accumulation of HM in phylloplane and leaves. Moreover, HM in the phylloplane was not from the internal transport of the plant but it could be due to the wind action or rains. Bacteria in phylloplane may have come from the soil due to their strong positive correlation with corresponding soil at the genus level. High HM level inhibited the relative abundance of dominant bacteria, increased the diversity and species richness of bacterial community in phylloplane, and induced more special bacteria to maintain higher productivity of the host plant, for which, Cu and Pb were the major contributors. Meanwhile, bacteria in phylloplane showed a universal positive correlation in the co-occurrence network, which showed less stability than that in corresponding soil in the smelting region, and it is helpful to regulate the growth of plants more rapidly. Nearly 25% of KEGG pathways were modulated by high HM level and bacterial function tended to stabilize HM to avoid the potential process of leaf absorption. The study illustrated that HM in phylloplane played an important role in shaping the bacterial community of phylloplane as compared to HM in leaves or phyllosphere, and the resulting increase of diversity and richness of bacterial community and special bacteria further maintained the growth of the host plant suffering from HM stress.
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Affiliation(s)
- Fanghan Qian
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xinjian Huang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yanyu Bao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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25
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Ji Y, Xu Y, Zhao M, Zhang G, Conrad R, Liu P, Feng Z, Ma J, Xu H. Winter drainage and film mulching cultivation mitigated CH 4 emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116194. [PMID: 36115239 DOI: 10.1016/j.jenvman.2022.116194] [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: 02/20/2022] [Revised: 08/09/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Winter flooding of harvested rice fields is a typical cropping system in mountainous areas, which emits considerable amounts of CH4. Plastic film mulching cultivation is recognized as an important rice cultivation practice in paddy field for water-saving irrigation. However, the effects of these managements on CH4 emissions in paddy soil and the underlying microbial mechanism are unclear. A field experiment was carried out with the application of winter drainage followed by traditional rice cultivation (WD), winter drainage followed by plastic film mulching cultivation (MC), as well as winter flooding followed by traditional rice cultivation (WF) as control in hilly paddy fields. We investigated the CH4 emissions, functional (CH4 production rate, 13C isotope) and structural (abundance, structure) responses of soil methanogenic archaeal and fermenting bacterial communities during rice season. Shifting the fields from WF into WD and MC substantially mitigated CH4 emissions by 62.3% and 59.2%, respectively, paralleled with the enhancement of soil Eh and the reductions of soil DOC content. Compared with WF, WD and MC both significantly decreased CH4 production rates and the copy numbers of mcrA gene. Moreover, an increasing contribution of hydrogenotrophic methanogenesis (from 30.7% to 50.0%) to total CH4 production was observed during the conversion from WF to MC under an anaerobic incubation, paralleled with the decreased acetate content and increased δ13C values of acetate-methyl and total acetate. The communities of methanogenic archaea and fermenting bacteria strongly responded to the shift from WF to WD, while MC only showed significant effects on the methanogenic archaeal communities. Compared with WF, WD and MC significantly increased the relative abundance of Methanothrix, Methanosarcina and Methanocella, while those of Methanoregula, Massilia and Geobacter were decreased. The co-occurrence networks showed that WD and MC induced the loss of mixed methanogenic fermentation modules, indicating the decrease in functional biodiversity and redundancy of fermenting bacterial and methanogenic archaeal communities.The findings suggest that WD and MC approach mitigate CH4 emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil, which represent the effective management strategies considering the water availability and CH4 mitigation in paddy-field agriculture.
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Affiliation(s)
- Yang Ji
- College of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yongji Xu
- College of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Mengying Zhao
- College of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Guangbin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China.
| | - Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Pengfei Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| | - Zhaozhong Feng
- College of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Jing Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Hua Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
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26
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Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion. Sci Rep 2022; 12:18684. [PMID: 36333419 PMCID: PMC9636222 DOI: 10.1038/s41598-022-22906-6] [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: 05/25/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Aquatic environments serve as a sink for anthropogenic discharges. A significant part of the discharge is tire wear, which is increasingly being released into the environment, causing environmental disasters due to their longevity and the large number of pollutants they contain. Main components of tires are plastic and zinc, which therefore can be used as substitutes for tire abrasion to study the effect on microbial life. We investigate environmentally realistic concentrations of plastic and zinc on a freshwater microeukaryotic community using high-throughput sequencing of the 18S V9 region over a 14-day exposure period. Apart from a generally unchanged diversity upon exposure to zinc and nanoplastics, a change in community structure due to zinc is evident, but not due to nanoplastics. Evidently, nanoplastic particles hardly affect the community, but zinc exposure results in drastic functional abundance shifts concerning the trophic mode. Phototrophic microorganisms were almost completely diminished initially, but photosynthesis recovered. However, the dominant taxa performing photosynthesis changed from bacillariophytes to chlorophytes. While phototrophic organisms are decreasing in the presence of zinc, the mixotrophic fraction initially benefitted and the heterotrophic fraction were benefitting throughout the exposure period. In contrast to lasting changes in taxon composition, the functional community composition is initially strongly imbalanced after application of zinc but returns to the original state.
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27
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Paramasivam K, Venkataraman K. Comparison of macro‐molluscan assemblages in a protected and a non‐protected tropical seagrass ecosystem. Biotropica 2022. [DOI: 10.1111/btp.13153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- K. Paramasivam
- Marine Biology Regional Centre Zoological Survey of India, Ministry of Environment, Forest and Climate Change (MoEFCC), Government of India Chennai India
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28
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Zengeya TA, Lombard RJ, Nelwamondo VE, Nunes AL, Measey J, Weyl OL. Trophic niche of an invasive generalist consumer: Australian redclaw crayfish,
Cherax quadricarinatus
, in the Inkomati River Basin, South Africa. AUSTRAL ECOL 2022. [DOI: 10.1111/aec.13230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tsungai Alfred Zengeya
- South African National Biodiversity Institute (SANBI), Kirstenbosch Research Centre Claremont 7735 South Africa
- Department of Zoology and Entomology, Centre for Invasion Biology University of Pretoria Pretoria South Africa
| | - Reuhl Jan‐Hendrik Lombard
- South African National Biodiversity Institute (SANBI), Kirstenbosch Research Centre Claremont 7735 South Africa
| | - Vhutali Ernest Nelwamondo
- Department of Zoology and Entomology, Centre for Invasion Biology University of Pretoria Pretoria South Africa
| | - Ana Luisa Nunes
- South African National Biodiversity Institute (SANBI), Kirstenbosch Research Centre Claremont 7735 South Africa
- Department of Botany and Zoology, Centre for Invasion Biology University of Stellenbosch Stellenbosch South Africa
- Centre for Invasion Biology South African Institute for Aquatic Biodiversity Makhanda South Africa
| | - John Measey
- Department of Botany and Zoology, Centre for Invasion Biology University of Stellenbosch Stellenbosch South Africa
| | - Olaf Lawrence Weyl
- Centre for Invasion Biology South African Institute for Aquatic Biodiversity Makhanda South Africa
- DST/NRF Research Chair in Inland Fisheries and Freshwater Ecology South African Institute for Aquatic Biodiversity Makhanda South Africa
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29
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Raynaud T, Devers-Lamrani M, Spor A, Blouin M. Community diversity determines the evolution of synthetic bacterial communities under artificial selection. Evolution 2022; 76:1883-1895. [PMID: 35789998 DOI: 10.1111/evo.14558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/20/2022] [Accepted: 06/17/2022] [Indexed: 01/22/2023]
Abstract
Artificial selection can be conducted at the community level in the laboratory through a differential propagation of the communities according to their level of expression of a targeted function. Working with communities instead of individuals as selection units brings in additional sources of variation in the considered function that can influence the outcome of the artificial selection. In this study, we wanted to assess the effect of manipulating the initial community richness on artificial selection efficiency, defined as the change in the targeted function over time. We applied artificial selection for a high productivity on synthetic bacterial communities varying for their richness (from one to 16 strains). Overall, the selected communities were 16% more productive than the control communities, but a convergence of community composition might have limited the effect of diversity on artificial selection efficiency. Community richness positively influenced community productivity and metabolic capacities and was a strong determinant of the dynamics of community evolution. We propose that applying artificial selection on communities varying for their diversity could be a way to find communities differing for their level of expression of a function but also for their responsiveness to artificial selection, provided that their initial composition is different enough.
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Affiliation(s)
- Tiffany Raynaud
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Marion Devers-Lamrani
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Aymé Spor
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Manuel Blouin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
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30
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Ren L, Lu Z, Xia X, Peng Y, Gong S, Song X, Jeppesen E, Han BP, Wu QL. Metagenomics reveals bacterioplankton community adaptation to long-term thermal pollution through the strategy of functional regulation in a subtropical bay. WATER RESEARCH 2022; 216:118298. [PMID: 35316678 DOI: 10.1016/j.watres.2022.118298] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Thermal effluents from coastal nuclear power plants have led to undesirable pollution and subsequent ecological impacts on local marine ecosystems. However, despite the ecological importance, we know little about the impacts on functionality of bacterioplankton subjected in systems with long-term thermal pollution. We used metagenomic sequencing to study of the effect of thermal pollution on bacterioplankton community metagenomics in summer in a subtropical bay located on the northern coast of the South China Sea. Thermal pollution (>15 y), which resulted in an increase in the summer seawater temperature around 8°C and caused seawater temperature up to approximate 39°C, significantly decreased bacterioplankton metabolic potentials in photosynthesis, organic carbon synthesis, and energy production. The bacterioplankton community metagenomics underwent a significant change in its structure from Synechococcus-dominant autotrophy to Alteromonas, Vibrio, and Pseudoalteromonas-dominated heterotrophy, and significantly up-regulated genes involved in organic compound degradation and dissimilatory nitrate reduction for the matter and energy acquisition under thermal pollution. Moreover, the bacterioplankton community metagenomics showed an up-regulation with heating of genes involved in DNA repair systems, heat shock responsive chaperones and proteins, and proteins involved in other biological processes, such as biofilm formation and the biosynthesis of unsaturated fatty acids and glycan, to adapt to the thermal environment. Collectively, it indicates a functional regulation of bacterioplankton adaptation to high-temperature stress, which might advance the understanding of the molecular mechanisms of community adaptation to global extreme warming in aquatic ecosystems.
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Affiliation(s)
- Lijuan Ren
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China; Key Laboratory of Tropical Marine Bio-resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Zhe Lu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yuyang Peng
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Sanqiang Gong
- Key Laboratory of Tropical Marine Bio-resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xingyu Song
- Key Laboratory of Tropical Marine Bio-resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Erik Jeppesen
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China; Department of Bioscience, Aarhus University, Silkeborg, Denmark; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara, Turkey; Institute of Marine Sciences, Middle East Technical University, Erdemli-Mersin, Turkey
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Qinglong L Wu
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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31
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Cheng WH, Hsieh CH, Chang CW, Shiah FK, Miki T. New index of functional specificity to predict the redundancy of ecosystem functions in microbial communities. FEMS Microbiol Ecol 2022; 98:6585974. [PMID: 35568503 DOI: 10.1093/femsec/fiac058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/14/2022] Open
Abstract
An ecosystem function is suggested to be more sensitive to biodiversity loss (i.e. low functional redundancy) when focusing on specific-type functions than broad-type functions. Thus far, specific-type functions have been loosely defined as functions performed by a small number of species (facilitative species) or functions involved in utilizing complex substrates. However, quantitative examination of functional specificity remains underexplored. We quantified the functional redundancy of 33 ecosystem functions in a freshwater system from 76 prokaryotic community samples over three years. For each function, we used a sparse regression model to estimate the number of facilitative Amplicon Sequence Variants (ASVs) and to define taxon-based functional specificity. We also used Bertz structural complexity to determine substrate-based functional specificity. We found that functional redundancy increased with the taxon-based functional specificity defined as the proportion of facilitative ASVs ( = facilitative ASV richness/ facilitative ASV richness + repressive ASV (ASVs reducing functioning) richness). When using substrate-based functional specificity, functional redundancy was influenced by Bertz complexity per se and by substrate acquisition mechanisms. Therefore, taxon-based functional specificity is a better predictive index for evaluating functional redundancy than substrate-based functional specificity. These findings provide a framework to quantitatively predict the consequences of diversity losses on ecosystem functioning.
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Affiliation(s)
- Wan-Hsuan Cheng
- Taiwan International Graduate Program (TIGP)-Earth System Science Program, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program (TIGP)-Earth System Science Program, National Central University, Taoyuan, Taiwan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Institute of Ecology and Evolutionary Biology, Department of Life Science, National Taiwan University, Taipei, Taiwan.,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.,National Center for Theoretical Sciences, Taipei, Taiwan
| | - Chun-Wei Chang
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.,National Center for Theoretical Sciences, Taipei, Taiwan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Takeshi Miki
- Department of Environmental Solution Technology, Faculty of Science and Technology, Ryukoku University, Seta, Shiga, Japan
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32
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Wang B, Allison SD. Climate-Driven Legacies in Simulated Microbial Communities Alter Litter Decomposition Rates. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.841824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mechanisms underlying diversity-functioning relationships have been a consistent area of inquiry in biogeochemistry since the 1950s. Though these mechanisms remain unresolved in soil microbiomes, many approaches at varying scales have pointed to the same notion—composition matters. Confronting the methodological challenge arising from the complexity of microbiomes, this study used the model DEMENTpy, a trait-based modeling framework, to explore trait-based drivers of microbiome-dependent litter decomposition. We parameterized DEMENTpy for five sites along a climate gradient in Southern California, United States, and conducted reciprocal transplant simulations analogous to a prior empirical study. The simulations demonstrated climate-dependent legacy effects of microbial communities on plant litter decomposition across the gradient. This result is consistent with the previous empirical study across the same gradient. An analysis of community-level traits further suggests that a 3-way tradeoff among resource acquisition, stress tolerance, and yield strategies influences community assembly. Simulated litter decomposition was predictable with two community traits (indicative of two of the three strategies) plus local environment, regardless of the system state (transient vs. equilibrium). Although more empirical confirmation is still needed, community traits plus local environmental factors (e.g., environment and litter chemistry) may robustly predict litter decomposition across spatial-temporal scales. In conclusion, this study offers a potential trait-based explanation for climate-dependent community effects on litter decomposition with implications for improved understanding of whole-ecosystem functioning across scales.
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33
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Diaz RM, Ernest SKM. Maintenance of community function through compensation breaks down over time in a desert rodent community. Ecology 2022; 103:e3709. [PMID: 35362169 PMCID: PMC9287087 DOI: 10.1002/ecy.3709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 11/08/2022]
Abstract
Understanding the ecological processes that maintain community function in systems experiencing species loss, and how these processes change over time, is key to understanding the relationship between community structure and function and predicting how communities may respond to perturbations in the Anthropocene. Using a 30‐year experiment on desert rodents, we show that the impact of species loss on community‐level energy use has changed repeatedly and dramatically over time, due to (1) the addition of new species to the community, and (2) a reduction in functional redundancy among the same set of species. Although strong compensation, initially driven by the dispersal of functionally redundant species to the local community, occurred in this system from 1997 to 2010, since 2010, compensation has broken down due to decreasing functional overlap within the same set of species. Simultaneously, long‐term changes in sitewide community composition due to niche complementarity have decoupled the dynamics of compensation from the overall impact of species loss on community‐level energy use. Shifting, context‐dependent compensatory dynamics, such as those demonstrated here, highlight the importance of explicitly long‐term, metacommunity, and eco‐evolutionary perspectives on the link between species‐level fluctuations and community function in a changing world.
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Affiliation(s)
- Renata M Diaz
- School of Natural Resources and Environment, University of Florida, Gainesville, FL
| | - S K Morgan Ernest
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
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Naidoo Y, Valverde A, Pierneef RE, Cowan DA. Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils. MICROBIAL ECOLOGY 2022; 83:689-701. [PMID: 34105010 DOI: 10.1007/s00248-021-01785-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Angel Valverde
- IRNASA-CSIC, C/Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
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35
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Chang CW, Miki T, Ye H, Souissi S, Adrian R, Anneville O, Agasild H, Ban S, Be'eri-Shlevin Y, Chiang YR, Feuchtmayr H, Gal G, Ichise S, Kagami M, Kumagai M, Liu X, Matsuzaki SIS, Manca MM, Nõges P, Piscia R, Rogora M, Shiah FK, Thackeray SJ, Widdicombe CE, Wu JT, Zohary T, Hsieh CH. Causal networks of phytoplankton diversity and biomass are modulated by environmental context. Nat Commun 2022; 13:1140. [PMID: 35241667 PMCID: PMC8894464 DOI: 10.1038/s41467-022-28761-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/11/2022] [Indexed: 11/21/2022] Open
Abstract
Untangling causal links and feedbacks among biodiversity, ecosystem functioning, and environmental factors is challenging due to their complex and context-dependent interactions (e.g., a nutrient-dependent relationship between diversity and biomass). Consequently, studies that only consider separable, unidirectional effects can produce divergent conclusions and equivocal ecological implications. To address this complexity, we use empirical dynamic modeling to assemble causal networks for 19 natural aquatic ecosystems (N24◦~N58◦) and quantified strengths of feedbacks among phytoplankton diversity, phytoplankton biomass, and environmental factors. Through a cross-system comparison, we identify macroecological patterns; in more diverse, oligotrophic ecosystems, biodiversity effects are more important than environmental effects (nutrients and temperature) as drivers of biomass. Furthermore, feedback strengths vary with productivity. In warm, productive systems, strong nitrate-mediated feedbacks usually prevail, whereas there are strong, phosphate-mediated feedbacks in cold, less productive systems. Our findings, based on recovered feedbacks, highlight the importance of a network view in future ecosystem management. Disentangling causal interactions among biodiversity, ecosystem functioning and environmental factors is key to understanding how ecosystems respond to changing environment. This study presents a global scale analysis quantifying causal interactions and feedbacks among phytoplankton diversity, biomass and nutrients along environmental gradients of aquatic ecosystems.
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Affiliation(s)
- Chun-Wei Chang
- National Center for Theoretical Sciences, Taipei, 10617, Taiwan.,Research Center for Environmental Changes, Academia Sinica, Taipei, 11529, Taiwan
| | - Takeshi Miki
- Faculty of Advanced Science and Technology, Ryukoku University, Otsu, Shiga, 520-2194, Japan.,Institute of Oceanography, National Taiwan University, Taipei, 10617, Taiwan.,Center for Biodiversity Science, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Hao Ye
- Health Science Center Libraries, University of Florida, Gainesville, FL, 32611, USA
| | - Sami Souissi
- Univ. Lille, CNRS, Univ, Littoral Côte D'Opale, IRD, UMR 8187, LOG- Laboratoire D'Océanologie et de Géosciences, Station Marine de Wimereux, F- 59000, Lille, France
| | - Rita Adrian
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, IGB, 12587, Berlin, Germany.,Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, 14195, Berlin, Germany
| | - Orlane Anneville
- National Research Institute for Agriculture, Food and Environment (INRAE), CARRTEL, Université Savoie Mont Blanc, 74200, Thonon les Bains, France
| | - Helen Agasild
- Centre for Limnology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, 51014, Tartu, Estonia
| | - Syuhei Ban
- Department of Ecosystem Studies, School of Environmental Science, The University of Shiga Prefecture, Hikone, 522-8533, Shiga, Japan
| | - Yaron Be'eri-Shlevin
- Kinneret Limnological Laboratory, Israel Oceanographic & Limnological Research, P.O. Box 447, 14950, Migdal, Israel
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Heidrun Feuchtmayr
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, Lancashire, LA1 4AP, UK
| | - Gideon Gal
- Kinneret Limnological Laboratory, Israel Oceanographic & Limnological Research, P.O. Box 447, 14950, Migdal, Israel
| | - Satoshi Ichise
- Lake Biwa Environmental Research Institute, Otsu, 520-0022, Japan
| | - Maiko Kagami
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, 240-8502, Kanagawa, Japan.,Department of Environmental Science, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Michio Kumagai
- Lake Biwa Environmental Research Institute, Otsu, 520-0022, Japan.,Research Center for Lake Biwa & Environmental Innovation, Ritsumeikan University, Kusatsu, 525-0058, Shiga, Japan
| | - Xin Liu
- Department of Ecosystem Studies, School of Environmental Science, The University of Shiga Prefecture, Hikone, 522-8533, Shiga, Japan
| | - Shin-Ichiro S Matsuzaki
- Biodiversity Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Marina M Manca
- CNR Water Research Institute (IRSA), L.go Tonolli 50, 28922, Verbania, Pallanza, Italy
| | - Peeter Nõges
- Centre for Limnology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, 51014, Tartu, Estonia
| | - Roberta Piscia
- CNR Water Research Institute (IRSA), L.go Tonolli 50, 28922, Verbania, Pallanza, Italy
| | - Michela Rogora
- CNR Water Research Institute (IRSA), L.go Tonolli 50, 28922, Verbania, Pallanza, Italy
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, 10617, Taiwan
| | - Stephen J Thackeray
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, Lancashire, LA1 4AP, UK
| | | | - Jiunn-Tzong Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tamar Zohary
- Kinneret Limnological Laboratory, Israel Oceanographic & Limnological Research, P.O. Box 447, 14950, Migdal, Israel
| | - Chih-Hao Hsieh
- National Center for Theoretical Sciences, Taipei, 10617, Taiwan. .,Research Center for Environmental Changes, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Oceanography, National Taiwan University, Taipei, 10617, Taiwan. .,Institute of Ecology and Evolutionary Biology, Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
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36
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Kocaoglu B, Alexander WH. Degeneracy measures in biologically plausible random Boolean networks. BMC Bioinformatics 2022; 23:71. [PMID: 35164672 PMCID: PMC8845291 DOI: 10.1186/s12859-022-04601-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Degeneracy—the ability of structurally different elements to perform similar functions—is a property of many biological systems. Highly degenerate systems show resilience to perturbations and damage because the system can compensate for compromised function due to reconfiguration of the underlying network dynamics. Degeneracy thus suggests how biological systems can thrive despite changes to internal and external demands. Although degeneracy is a feature of network topologies and seems to be implicated in a wide variety of biological processes, research on degeneracy in biological networks is mostly limited to weighted networks. In this study, we test an information theoretic definition of degeneracy on random Boolean networks, frequently used to model gene regulatory networks. Random Boolean networks are discrete dynamical systems with binary connectivity and thus, these networks are well-suited for tracing information flow and the causal effects. By generating networks with random binary wiring diagrams, we test the effects of systematic lesioning of connections and perturbations of the network nodes on the degeneracy measure. Results Our analysis shows that degeneracy, on average, is the highest in networks in which ~ 20% of the connections are lesioned while 50% of the nodes are perturbed. Moreover, our results for the networks with no lesions and the fully-lesioned networks are comparable to the degeneracy measures from weighted networks, thus we show that the degeneracy measure is applicable to different networks. Conclusions Such a generalized applicability implies that degeneracy measures may be a useful tool for investigating a wide range of biological networks and, therefore, can be used to make predictions about the variety of systems’ ability to recover function. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04601-5.
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Affiliation(s)
- Basak Kocaoglu
- Center for Complex Systems and Brain Sciences, Florida Atlantic University, Boca Raton, FL, USA. .,The Brain Institute, Florida Atlantic University, Jupiter, FL, 33431, USA.
| | - William H Alexander
- Center for Complex Systems and Brain Sciences, Florida Atlantic University, Boca Raton, FL, USA.,Department of Psychology, Florida Atlantic University, Boca Raton, FL, USA.,The Brain Institute, Florida Atlantic University, Jupiter, FL, 33431, USA
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37
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Polazzo F, Roth SK, Hermann M, Mangold‐Döring A, Rico A, Sobek A, Van den Brink PJ, Jackson M. Combined effects of heatwaves and micropollutants on freshwater ecosystems: Towards an integrated assessment of extreme events in multiple stressors research. GLOBAL CHANGE BIOLOGY 2022; 28:1248-1267. [PMID: 34735747 PMCID: PMC9298819 DOI: 10.1111/gcb.15971] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/14/2021] [Accepted: 10/29/2021] [Indexed: 05/11/2023]
Abstract
Freshwater ecosystems are strongly influenced by weather extremes such as heatwaves (HWs), which are predicted to increase in frequency and magnitude in the future. In addition to these climate extremes, the freshwater realm is impacted by the exposure to various classes of chemicals emitted by anthropogenic activities. Currently, there is limited knowledge on how the combined exposure to HWs and chemicals affects the structure and functioning of freshwater ecosystems. Here, we review the available literature describing the single and combined effects of HWs and chemicals on different levels of biological organization, to obtain a holistic view of their potential interactive effects. We only found a few studies (13 out of the 61 studies included in this review) that investigated the biological effects of HWs in combination with chemical pollution. The reported interactive effects of HWs and chemicals varied largely not only within the different trophic levels but also depending on the studied endpoints for populations or individuals. Hence, owing also to the little number of studies available, no consistent interactive effects could be highlighted at any level of biological organization. Moreover, we found an imbalance towards single species and population experiments, with only five studies using a multitrophic approach. This results in a knowledge gap for relevant community and ecosystem level endpoints, which prevents the exploration of important indirect effects that can compromise food web stability. Moreover, this knowledge gap impairs the validity of chemical risk assessments and our ability to protect ecosystems. Finally, we highlight the urgency of integrating extreme events into multiple stressors studies and provide specific recommendations to guide further experimental research in this regard.
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Affiliation(s)
- Francesco Polazzo
- IMDEA Water Institute, Science and Technology Campus of the University of AlcaláAlcalá de HenaresSpain
| | - Sabrina K. Roth
- Department of Environmental ScienceStockholm UniversityStockholmSweden
| | - Markus Hermann
- Aquatic Ecology and Water Quality Management GroupWageningen UniversityWageningenThe Netherlands
| | - Annika Mangold‐Döring
- Aquatic Ecology and Water Quality Management GroupWageningen UniversityWageningenThe Netherlands
| | - Andreu Rico
- IMDEA Water Institute, Science and Technology Campus of the University of AlcaláAlcalá de HenaresSpain
- Cavanilles Institute of Biodiversity and Evolutionary BiologyUniversity of ValenciaValenciaSpain
| | - Anna Sobek
- Department of Environmental ScienceStockholm UniversityStockholmSweden
| | - Paul J. Van den Brink
- Aquatic Ecology and Water Quality Management GroupWageningen UniversityWageningenThe Netherlands
- Wageningen Environmental ResearchWageningenThe Netherlands
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38
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Fenoy E, Pradhan A, Pascoal C, Rubio-Ríos J, Batista D, Moyano-López FJ, Cássio F, Casas JJ. Elevated temperature may reduce functional but not taxonomic diversity of fungal assemblages on decomposing leaf litter in streams. GLOBAL CHANGE BIOLOGY 2022; 28:115-127. [PMID: 34651383 DOI: 10.1111/gcb.15931] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/02/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Mounting evidence points to a linkage between biodiversity and ecosystem functioning (B-EF). Global drivers, such as warming and nutrient enrichment, can alter species richness and composition of aquatic fungal assemblages associated with leaf-litter decomposition, a key ecosystem process in headwater streams. However, effects of biodiversity changes on ecosystem functions might be countered by the presumed high functional redundancy of fungal species. Here, we examined how environmental variables and leaf-litter traits (based on leaf chemistry) affect taxonomic and functional α- and β-diversity of fungal decomposers. We analysed taxonomic diversity (DNA-fingerprinting profiles) and functional diversity (community-level physiological profiles) of fungal communities in four leaf-litter species from four subregions differing in stream-water characteristics and riparian vegetation. We hypothesized that increasing stream-water temperature and nutrients would alter taxonomic diversity more than functional diversity due to the functional redundancy among aquatic fungi. Contrary to our expectations, fungal taxonomic diversity varied little with stream-water characteristics across subregions, and instead taxon replacement occurred. Overall taxonomic β-diversity was fourfold higher than functional diversity, suggesting a high degree of functional redundancy among aquatic fungi. Elevated temperature appeared to boost assemblage uniqueness by increasing β-diversity while the increase in nutrient concentrations appeared to homogenize fungal assemblages. Functional richness showed a negative relationship with temperature. Nonetheless, a positive relationship between leaf-litter decomposition and functional richness suggests higher carbon use efficiency of fungal communities in cold waters.
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Affiliation(s)
- Encarnación Fenoy
- Department of Biology and Geology, University of Almería, Almería, Spain
- Andalusian Centre for Assessment and Monitoring of Global Change (CAESCG), Almería, Spain
| | - Arunava Pradhan
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability, University of Minho, Braga, Portugal
| | - Cláudia Pascoal
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability, University of Minho, Braga, Portugal
| | - Juan Rubio-Ríos
- Department of Biology and Geology, University of Almería, Almería, Spain
- Andalusian Centre for Assessment and Monitoring of Global Change (CAESCG), Almería, Spain
| | - Daniela Batista
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability, University of Minho, Braga, Portugal
| | | | - Fernanda Cássio
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability, University of Minho, Braga, Portugal
| | - J Jesús Casas
- Department of Biology and Geology, University of Almería, Almería, Spain
- Andalusian Centre for Assessment and Monitoring of Global Change (CAESCG), Almería, Spain
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39
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Li J, Zhu T, Singh BK, Pendall E, Li B, Fang C, Nie M. Key microorganisms mediate soil carbon-climate feedbacks in forest ecosystems. Sci Bull (Beijing) 2021; 66:2036-2044. [PMID: 36654173 DOI: 10.1016/j.scib.2021.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/05/2021] [Accepted: 03/05/2021] [Indexed: 02/03/2023]
Abstract
Soil microorganisms are known to significantly contribute to climate change through soil carbon (C) cycle feedbacks. However, it is challenging to incorporate these feedbacks into predictions of future patterns of terrestrial C cycling, largely because of the vast diversity of soil microorganisms and their responses to environmental conditions. Here, we show that the composition of the bacterial community can provide information about the microbial community-level thermal response (MCTR), which drives ecosystem-scale soil C-climate feedbacks. The dominant taxa from 169 sites representing a gradient from tropical to boreal forest mainly belonged to the phyla Actinobacteria and Acidobacteria. Moreover, we show that the MCTR in warm biomes and acidic soils was linked primarily to bacteria, whereas the MCTR in cold biomes and alkaline soils was primarily associated with fungi. Our results provide strong empirical evidence of linkages between microbial composition and the MCTR across a wide range of forests, and suggest the importance of specific microorganisms in regulating soil C-climate feedbacks.
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Affiliation(s)
- Jinquan Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ting Zhu
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Penrith NSW 2751, Australia
| | - Elise Pendall
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia
| | - Bo Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Changming Fang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ming Nie
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
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40
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Saraiva JP, Bartholomäus A, Kallies R, Gomes M, Bicalho M, Coelho Kasmanas J, Vogt C, Chatzinotas A, Stadler P, Dias O, Nunes da Rocha U. OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes. Life Sci Alliance 2021; 4:4/12/e202101167. [PMID: 34580179 PMCID: PMC8500227 DOI: 10.26508/lsa.202101167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/01/2022] Open
Abstract
OrtSuite predicts synergistic species interactions using the genomic potential of microbial communities The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.
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Affiliation(s)
- João Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | | | - René Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Marta Gomes
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Marcos Bicalho
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jonas Coelho Kasmanas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Institute of Mathematics and Computer Sciences, University of Sao Paulo, Sao Carlos, Brazil.,Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, and Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, University of Leipzig, Leipzig, Germany
| | - Carsten Vogt
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Peter Stadler
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, and Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.,Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.,Santa Fe Institute, Santa Fe, NM, USA
| | - Oscar Dias
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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41
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Deng M, Liu W, Li P, Jiang L, Li S, Jia Z, Yang S, Guo L, Wang Z, Liu L. Intraspecific trait variation drives grassland species richness and productivity under changing precipitation. Ecosphere 2021. [DOI: 10.1002/ecs2.3707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Meifeng Deng
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Xiangshan Beijing 100093 China
- University of Chinese Academy of Sciences Yuquanlu Beijing 100049 China
| | - Weixing Liu
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Xiangshan Beijing 100093 China
- University of Chinese Academy of Sciences Yuquanlu Beijing 100049 China
| | - Ping Li
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Xiangshan Beijing 100093 China
- University of Chinese Academy of Sciences Yuquanlu Beijing 100049 China
| | - Lin Jiang
- School of Biology Georgia Institute of Technology 310 Ferst Drive Atlanta Georgia 30332 USA
| | - Shaopeng Li
- School of Ecological and Environmental Sciences East China Normal University Minxing Shanghai 200241 China
| | - Zhou Jia
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Xiangshan Beijing 100093 China
- University of Chinese Academy of Sciences Yuquanlu Beijing 100049 China
| | - Sen Yang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Xiangshan Beijing 100093 China
- University of Chinese Academy of Sciences Yuquanlu Beijing 100049 China
| | - Lulu Guo
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Xiangshan Beijing 100093 China
- University of Chinese Academy of Sciences Yuquanlu Beijing 100049 China
| | - Zhenhua Wang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Xiangshan Beijing 100093 China
- University of Chinese Academy of Sciences Yuquanlu Beijing 100049 China
| | - Lingli Liu
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Xiangshan Beijing 100093 China
- University of Chinese Academy of Sciences Yuquanlu Beijing 100049 China
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42
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Gjini E, Madec S. The ratio of single to co-colonization is key to complexity in interacting systems with multiple strains. Ecol Evol 2021; 11:8456-8474. [PMID: 34257910 PMCID: PMC8258234 DOI: 10.1002/ece3.7259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 12/16/2020] [Accepted: 01/12/2021] [Indexed: 11/06/2022] Open
Abstract
The high number and diversity of microbial strains circulating in host populations have motivated extensive research on the mechanisms that maintain biodiversity. However, much of this work focuses on strain-specific and cross-immunity interactions. Another less explored mode of pairwise interaction is via altered susceptibilities to co-colonization in hosts already colonized by one strain. Diversity in such interaction coefficients enables strains to create dynamically their niches for growth and persistence, and "engineer" their common environment. How such a network of interactions with others mediates collective coexistence remains puzzling analytically and computationally difficult to simulate. Furthermore, the gradients modulating stability-complexity regimes in such multi-player endemic systems remain poorly understood. In a recent study (Madec & Gjini, Bulletin of Mathematical Biology, 82), we obtained an analytic representation for N-type coexistence in an SIS epidemiological model with co-colonization. We mapped multi-strain dynamics to a replicator equation using timescale separation. Here, we examine what drives coexistence regimes in such co-colonization system. We find the ratio of single to co-colonization, µ, critically determines the type of equilibrium and number of coexisting strains, and encodes a trade-off between overall transmission intensity R 0 and mean interaction coefficient in strain space, k. Preserving a given coexistence regime, under fixed trait variation, requires balancing between higher mean competition in favorable environments, and higher cooperation in harsher environments, and is consistent with the stress gradient hypothesis. Multi-strain coexistence tends to steady-state attractors for small µ, whereas as µ increases, dynamics tend to more complex attractors. Following strain frequencies, evolutionary dynamics in the system also display contrasting patterns with µ, interpolating between multi-stable and fluctuating selection for cooperation and mean invasion fitness, in the two extremes. This co-colonization framework could be applied more generally, to study invariant principles in collective coexistence, and to quantify how critical shifts in community dynamics get potentiated by mean-field and environmental gradients.
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Affiliation(s)
- Erida Gjini
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Center for Computational and Stochastic MathematicsInstituto Superior TécnicoUniversity of LisbonLisbonPortugal
| | - Sten Madec
- Institut Denis PoissonUniversity of ToursToursFrance
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Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures. BIOLOGY 2021; 10:biology10070569. [PMID: 34206701 PMCID: PMC8301126 DOI: 10.3390/biology10070569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 11/26/2022]
Abstract
Simple Summary The study of a microbial community nowadays mostly relies on environmental DNA (eDNA)-based amplicon sequencing. However, some studies report that this method is not able to capture all bacterial taxa in the community. This study presents an enrichment culture-based amplicon sequencing method to estimate the proportion of culturable bacteria in soil. A bacterial community derived from this method was compared with those derived from culture-independent methods (eDNA-based amplicon sequencing). This study revealed that the majority of cultured bacteria were rare or completely absent in the community detected by the culture-independent method. Nevertheless, the dominant bacterial Operational Taxonomic Units (OTUs) were also observed, as 8 out of the 30 most frequently detected bacteria from eDNA were found in the enrichment cultures. The method proposed in this study could extend bacterial community’s information derived from the culture-independent method. Furthermore, the enrichment culture-based amplicon sequencing method could be a promising tool for quick screening of a culturable bacterial community and its associated function for various applications. Abstract This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.
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Li Y, Ge Y, Wang J, Shen C, Wang J, Liu YJ. Functional redundancy and specific taxa modulate the contribution of prokaryotic diversity and composition to multifunctionality. Mol Ecol 2021; 30:2915-2930. [PMID: 33905157 DOI: 10.1111/mec.15935] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/29/2022]
Abstract
Observational and experimental evidence has revealed the functional importance of microbial diversity. However, the effects of microbial diversity loss on ecosystem functions are not consistent across studies, which are probably tempered by microbial functional redundancy, specific taxa and functions evaluated. Here we conducted diversity manipulation experiments in two independent soils with distinct prokaryotic communities, and investigated how the initial community traits (e.g., distinct functional redundancy and taxonomic composition) modulate the contribution of prokaryotic diversity loss and composition shift to eight ecosystem functions related to soil nutrient cycling. We found that diversity loss impaired three functions (potential nitrification rate, N2 -fixation activity and phosphatase) and multifunctionality only in the communities with low functional redundancy, but all examined functions were unaffected in the communities with high functional redundancy. All significantly affected functions belonged to specialized functions, while the broad function (soil basal respiration) was unaffected. Moreover, prokaryotic composition explained more functional variation than diversity, which was ascribed to the crucial role of specific taxa that influence particular functions. Taken together, this study provides empirical evidence for identifying the mechanism underlying the ecosystem response to changes in microbial community, with implications for improving the prediction of ecosystem process models and managing microbial communities to promote ecosystem services.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianlei Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yong-Jun Liu
- Key Laboratory of Pollinating Insect Biology, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
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Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
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Mugge RL, Salerno JL, Hamdan LJ. Microbial Functional Responses in Marine Biofilms Exposed to Deepwater Horizon Spill Contaminants. Front Microbiol 2021; 12:636054. [PMID: 33717029 PMCID: PMC7947620 DOI: 10.3389/fmicb.2021.636054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
Marine biofilms are essential biological components that transform built structures into artificial reefs. Anthropogenic contaminants released into the marine environment, such as crude oil and chemical dispersant from an oil spill, may disrupt the diversity and function of these foundational biofilms. To investigate the response of marine biofilm microbiomes from distinct environments to contaminants and to address microbial functional response, biofilm metagenomes were analyzed from two short-term microcosms, one using surface seawater (SSW) and the other using deep seawater (DSW). Following exposure to crude oil, chemical dispersant, and dispersed oil, taxonomically distinct communities were observed between microcosms from different source water challenged with the same contaminants and higher Shannon diversity was observed in SSW metagenomes. Marinobacter, Colwellia, Marinomonas, and Pseudoalteromonas phylotypes contributed to driving community differences between SSW and DSW. SSW metagenomes were dominated by Rhodobacteraceae, known biofilm-formers, and DSW metagenomes had the highest abundance of Marinobacter, associated with hydrocarbon degradation and biofilm formation. Association of source water metadata with treatment groups revealed that control biofilms (no contaminant) harbor the highest percentage of significant KEGG orthologs (KOs). While 70% functional similarity was observed among all metagenomes from both experiments, functional differences between SSW and DSW metagenomes were driven primarily by membrane transport KOs, while functional similarities were attributed to translation and signaling and cellular process KOs. Oil and dispersant metagenomes were 90% similar to each other in their respective experiments, which provides evidence of functional redundancy in these microbiomes. When interrogating microbial functional redundancy, it is crucial to consider how composition and function evolve in tandem when assessing functional responses to changing environmental conditions within marine biofilms. This study may have implications for future oil spill mitigation strategies at the surface and at depth and also provides information about the microbiome functional responses of biofilms on steel structures in the marine built environment.
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Affiliation(s)
- Rachel L Mugge
- Division of Coastal Sciences, School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, MS, United States
| | - Jennifer L Salerno
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, United States
| | - Leila J Hamdan
- Division of Coastal Sciences, School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, MS, United States
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Massello FL, Donati E. Effect of heavy metal-induced stress on two extremophilic microbial communities from Caviahue-Copahue, Argentina. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115709. [PMID: 33010675 DOI: 10.1016/j.envpol.2020.115709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 09/03/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Metal pollution is a great concern worldwide and the development of new technologies for more sustainable extraction methods as well as for the remediation of polluted sites is essential. Extremophilic microorganisms are attractive for this purpose since they have poly-resistance mechanisms which make them versatile. In this work, we sampled an acidic river and a hot spring of Caviahue-Copahue volcanic environment. The indigenous microbial communities were exposed to five heavy metals (Cd, Co, Cu, Ni and Zn) in batch-cultures favouring different metabolisms of biotechnological interest. Remarkably, high tolerance values were reached in all the cultures, even though most of the metals studied were not present in the environmental sample. Particularly, outstanding tolerances were exhibited by acidophiles, which grew at concentrations as high as 400 mM of Zn and Ni. High-throughput amplicon sequencing of 16S rRNA gene was used to study the indigenous communities and the resistant consortia. We took three approaches for the analysis: phylotypes, OTUs and amplicon sequence variants (ASVs). Interestingly, similar conclusions were drawn in all three cases. Analysing the phylogenetic structure and functional potential of the adapted consortia, we found that the strongest selection was exerted by the culture media. Notably, there was a poor correlation between alpha diversity and metal stress; furthermore, metal stress did not seem to harm the functional potential of the consortia. All these results reveal a great adaptability and versatility. At the end, 25 metal-resistant extremophilic consortia with potential uses in bioremediation, bioleaching or biomonitoring processes were obtained.
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Affiliation(s)
- Francisco L Massello
- CINDEFI (CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - Edgardo Donati
- CINDEFI (CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
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Contrasting Environmental Drivers Determine Biodiversity Patterns in Epiphytic Lichen Communities along a European Gradient. Microorganisms 2020; 8:microorganisms8121913. [PMID: 33271812 PMCID: PMC7760525 DOI: 10.3390/microorganisms8121913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 11/23/2022] Open
Abstract
Assessing the ecological impacts of environmental change on biological communities requires knowledge of the factors driving the spatial patterns of the three diversity facets along extensive environmental gradients. We quantified the taxonomic (TD), functional (FD), and phylogenetic diversity (PD) of lichen epiphytic communities in 23 beech forests along Europe to examine their response to environmental variation (climate, habitat quality, spatial predictors) at a continental geographic scale. We selected six traits related to the climatic conditions in forest ecosystems, the water-use strategy and the nutrient uptake, and we built a phylogenetic tree based on four molecular markers. FD and climate determined TD and PD, with spatial variables also affecting PD. The three diversity facets were primarily shaped by distinct critical predictors, with the temperature diurnal range affecting FD and PD, and precipitation of the wettest month determining TD. Our results emphasize the value of FD for explaining part of TD and PD variation in lichen communities at a broad geographic scale, while highlighting that these diversity facets provide complementary information about the communities’ response under changing environmental conditions. Furthermore, traits such as growth form, photobiont type, and reproductive strategy mediated the response of lichen communities to abiotic factors emerging as useful indicators of macroclimatic variations.
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Six-year removal of co-dominant grasses alleviated competitive pressure on subdominant grasses but dominant shrub removal had neutral effects in a subalpine ecosystem. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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50
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Avila-Jimenez ML, Burns G, He Z, Zhou J, Hodson A, Avila-Jimenez JL, Pearce D. Functional Associations and Resilience in Microbial Communities. Microorganisms 2020; 8:microorganisms8060951. [PMID: 32599781 PMCID: PMC7357002 DOI: 10.3390/microorganisms8060951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022] Open
Abstract
Microbial communities have inherently high levels of metabolic flexibility and functional redundancy, yet the structure of microbial communities can change rapidly with environmental perturbation. To understand whether such changes observed at the taxonomic level translate into differences at the functional level, we analyzed the structure of taxonomic and functional gene distribution across Arctic and Antarctic locations. Taxonomic diversity (in terms of alpha diversity and species richness) differed significantly with location. However, we found that functional genes distributed evenly across bacterial networks and that this functional distribution was also even across different geographic locations. For example, on average 15% of the functional genes were related to carbon cycling across all bacterial networks, slightly over 21% of the genes were stress-related and only 0.5% of the genes were linked to carbon degradation functions. In such a distribution, each bacterial network includes all of the functional groups distributed following the same proportions. However, the total number of functional genes that is included in each bacterial network differs, with some clusters including many more genes than others. We found that the proportion of times a specific gene must occur to be linked to a specific cluster is 8%, meaning the relationship between the total number of genes in the cluster and the number of genes per function follows a linear pattern: smaller clusters require a gene to appear less frequently to get fixed within the cluster, while larger clusters require higher gene frequencies. We suggest that this mechanism of functional association between equally rare or equally abundant genes could have implications for ecological resilience, as non-dominant genes also associate in fully functioning ecological networks, potentially suggesting that there are always pre-existing functional networks available to exploit new ecological niches (where they can become dominant) as they emerge; for example, in the case of rapid or sudden environmental change. Furthermore, this pattern did not correlate with taxonomic distribution, suggesting that bacteria associate based on functionality and this is independent of its taxonomic position. Our analyses based on ecological networks also showed no clear evidence of recent environmental impact on polar marine microbial communities at the functional level, unless all communities analyzed have changed exactly in the same direction and intensity, which is unlikely given we are comparing areas changing at different rates.
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Affiliation(s)
| | - Gavin Burns
- British Antarctic Survey, Cambridge CB3 0ET, UK;
| | - Zhili He
- Department of Microbiology and Plant Science, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA; (Z.H.); (J.Z.)
- Environmental Microbiomics Research Center and School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Science, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA; (Z.H.); (J.Z.)
| | - Andrew Hodson
- Geology Department, University Centre in Svalbard, 9171 Longyearbyen, Norway;
- Department of Environmental Sciences, Western Norway University of Applied Sciences, Røyrgata 6, N-6856 Sogndal, Norway
| | - Jose-Luis Avila-Jimenez
- Department of Informatics and Numerical Analysis, University of Cordoba, Campus Universitario de Rabanales, Carretera Nacional IV, Km. 396. C.P. 14014 Cordoba, Spain;
| | - David Pearce
- British Antarctic Survey, Cambridge CB3 0ET, UK;
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle (UK), Ellison Building, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
- Correspondence:
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