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Sochor M, Duchoslav M, Forejtová V, Hroneš M, Konečná M, Trávníček B. Distinct geographic parthenogenesis in spite of niche conservatism and a single ploidy level: A case of Rubus ser. Glandulosi (Rosaceae). New Phytol 2024; 242:1348-1362. [PMID: 38407427 DOI: 10.1111/nph.19618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
Asexual organisms often differ in their geographic distributions from their sexual relatives. This phenomenon, termed geographic parthenogenesis, has long been known, but the underlying factors behind its diverse patterns have been under dispute. Particularly problematic is an association between asexuality and polyploidy in most taxa. Here, we present a new system of geographic parthenogenesis on the tetraploid level, promising new insights into this complex topic. We used flow cytometric seed screen and microsatellite genotyping to characterise the patterns of distribution of sexuals and apomicts and genotypic distributions in Rubus ser. Glandulosi across its range. Ecological modelling and local-scale vegetation and soil analyses were used to test for niche differentiation between the reproductive groups. Apomicts were detected only in North-western Europe, sexuals in the rest of the range in Europe and West Asia, with a sharp borderline stretched across Central Europe. Despite that, we found no significant differences in ecological niches. Genotypic richness distributions suggested independence of the reproductive groups and a secondary contact. We argue that unless a niche differentiation (resulting from polyploidy and/or hybridity) evolves, the main factors behind the patterns of geographic parthenogenesis in plants are phylogeographic history and neutral microevolutionary processes, such as clonal turnover.
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Affiliation(s)
- Michal Sochor
- Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Šlechtitelů 29, Olomouc, 78371, Czech Republic
| | - Martin Duchoslav
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Věra Forejtová
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
- Station of Apple Breeding for Disease Resistance, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 313, Prague 6-Lysolaje, 16502, Czech Republic
| | - Michal Hroneš
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Michaela Konečná
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Bohumil Trávníček
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
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Umarani MS, Wang D, O'Dwyer JP, D'Andrea R. A Spatial Signal of Niche Differentiation in Tropical Forests. Am Nat 2024; 203:445-457. [PMID: 38489774 DOI: 10.1086/729218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
AbstractExplaining diversity in tropical forests remains a challenge in community ecology. Theory tells us that species differences can stabilize communities by reducing competition, while species similarities can promote diversity by reducing fitness differences and thus prolonging the time to competitive exclusion. Combined, these processes may lead to clustering of species such that species are niche differentiated across clusters and share a niche within each cluster. Here, we characterize this partial niche differentiation in a tropical forest in Panama by measuring spatial clustering of woody plants and relating these clusters to local soil conditions. We find that species were spatially clustered and the clusters were associated with specific concentrations of soil nutrients, reflecting the existence of nutrient niches. Species were almost twice as likely to recruit in their own nutrient niche. A decision tree algorithm showed that local soil conditions correctly predicted the niche of the trees with up to 85% accuracy. Iron, zinc, phosphorus, manganese, and soil pH were among the best predictors of species clusters.
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Sripontan Y, Wanthathaen C, Chiu CI. Fitness consequences of intraguild predation between Spodoptera frugiperda (Lepidoptera: Noctuidae) and Ostrinia furnacalis (Lepidoptera: Crambidae). J Econ Entomol 2024; 117:145-155. [PMID: 38167994 DOI: 10.1093/jee/toad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
The introduction of the fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), into Thailand has significantly altered the dynamics of maize pests. It has overshadowed Ostrinia furnacalis (Guenée) (Asian corn borer) (Lepidoptera: Crambidae), previously the most severe maize insect in Thailand. This transition is postulated to stem from the superior intraguild predation (IGP) capabilities of S. frugiperda. To validate this supposition, we assessed the co-distribution patterns and damage locales of both pests within maize fields and analyzed the IGP's repercussions on their larval growth, survival, and fecundity. Our findings demonstrate that: (i) incidence of O. furnacalis in maize fields is markedly reduced following the introduction of S. frugiperda; (ii) abundance of S. frugiperda and O. furnacalis is negatively correlated in field; (iii) interspecific interactions affect the spatial distributions of S. frugiperda and O. furnacalis on shared plants; (iv) S. frugiperda has lower generation time and higher fecundity; and (v) IGP amplifies the growth rate of S. frugiperda and elevates mortality in O. furnacalis. Moreover, in response to the competitive pressure exerted by S. frugiperda, O. furnacalis exhibited expedited molting and growth without a commensurate increase in size. Our data suggest IGP proficiency underpins S. frugiperda's dominance in Thai maize fields. We propose a niche differentiation on spatiotemporal distribution facilitating the coexistence of S. frugiperda and O. furnacalis. The impact of S. frugiperda on pest management strategies is discussed.
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Affiliation(s)
- Yuwatida Sripontan
- Entomology and Plant Pathology Section, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | - Chatchaton Wanthathaen
- Entomology and Plant Pathology Section, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | - Chun-I Chiu
- Entomology and Plant Pathology Department, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
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Zhang Z, Bi J, Zhao X, Cai Y, Yang C. Comparison of Reproductive Strategies between Two Sympatric Copsychus Passerines. Animals (Basel) 2024; 14:554. [PMID: 38396520 PMCID: PMC10885907 DOI: 10.3390/ani14040554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Reproduction plays a crucial role in determining the development, fate, and dynamics of bird populations. However, reproductive strategies vary among species and populations. In this study, we investigated the reproductive strategies of the Oriental Magpie Robin (Copsychus saularis) and White-rumped Shama (C. malabarica), which are closely related passerines that reproduce in sympatric areas. We found that although these two species were both cavity nesting, their nest-site selection differed; the Shama preferred nesting close to trees and forests, whereas the Magpie Robin nested close to human residential areas. Furthermore, their egg incubation patterns differed; the Shama increased daily incubation frequency with incubation time, but the Magpie Robin maintained its daily incubation time regardless of changes in incubation frequency. However, the nestling heating patterns of these two species were similar, indicating a critical demand for regulating hatchling body temperature during this crucial stage. The feeding frequencies of male parents were strongly correlated with those of females in both species, suggesting equal contribution and good synchronization between the sexes. Nestling feeding frequency was also correlated with nest cleaning frequency, implying coordination between feeding and defecation by parents and offspring, respectively. This research explored the divergence and convergence of reproductive strategies between these two sympatric species, providing valuable insights into the niche differentiation theory.
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Affiliation(s)
| | | | | | - Yan Cai
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Canchao Yang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China
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Pasciullo Boychuck S, Brenner LJ, Gagorik CN, Schamel JT, Baker S, Tran E, vonHoldt BM, Koepfli K, Maldonado JE, DeCandia AL. The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations. Ecol Evol 2024; 14:e11017. [PMID: 38362164 PMCID: PMC10867392 DOI: 10.1002/ece3.11017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024] Open
Abstract
California's Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine-scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco-evolutionary processes enable the coexistence of terrestrial carnivores-and their microbiomes-in island environments.
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Affiliation(s)
| | | | | | | | | | - Elton Tran
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | | | - Klaus‐Peter Koepfli
- Center for Species SurvivalSmithsonian's National Zoo & Conservation Biology InstituteFront RoyalVirginiaUSA
- Smithsonian‐Mason School of ConservationGeorge Mason UniversityFront RoyalVirginiaUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian's National Zoo & Conservation Biology InstituteWashingtonDCUSA
| | - Alexandra L. DeCandia
- Biology, Georgetown UniversityWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian's National Zoo & Conservation Biology InstituteWashingtonDCUSA
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Yu J, Lee JYY, Tang SN, Lee PKH. Niche differentiation in microbial communities with stable genomic traits over time in engineered systems. ISME J 2024; 18:wrae042. [PMID: 38470313 PMCID: PMC10987969 DOI: 10.1093/ismejo/wrae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/21/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Kowloon, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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Davison J, Gerz M, Hiiesalu I, Moora M, Semchenko M, Zobel M. Niche types and community assembly. Ecol Lett 2024; 27:e14327. [PMID: 37819920 DOI: 10.1111/ele.14327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Studies of niche differentiation and biodiversity often focus on a few niche dimensions due to the methodological challenge of describing hyperdimensional niche space. However, this may limit our understanding of community assembly processes. We used the full spectrum of realized niche types to study arbuscular mycorrhizal fungal communities: distinguishing abiotic and biotic, and condition and resource, axes. Estimates of differentiation in relation to different niche types were only moderately correlated. However, coexisting taxon niches were consistently less differentiated than expected, based on a regional null model, indicating the importance of habitat filtering at that scale. Nonetheless, resource niches were relatively more differentiated than condition niches, which is consistent with the effect of a resource niche-based coexistence mechanism. Considering niche types, and in particular distinguishing resource and condition niches, provides a more complete understanding of community assembly, compared with studying individual niche axes or the full niche.
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Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maret Gerz
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Albert PJ, Reuman DC. Asymmetric relationships and their effects on coexistence. Ecol Lett 2024; 27:e14334. [PMID: 37957830 DOI: 10.1111/ele.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023]
Abstract
Species coexistence attracts wide interest in ecology. Modern coexistence theory (MCT) identifies coexistence mechanisms, one of which, storage effects, hinges on relationships between fluctuations in environmental and competitive pressures. However, such relationships are typically measured using covariance, which does not account for the possibility that environment and competition may be more related to each other when they are strong than when weak, or vice versa. Recent work showed that such 'asymmetric tail associations' (ATAs) are common between ecological variables, and are important for extinction risk, ecosystem stability, and other phenomena. We extend MCT, decomposing storage effects to show the influence of ATAs. Analysis of a simple model and an empirical example using diatoms illustrate that ATA influences can be comparable in magnitude to other mechanisms of coexistence and that ATAs can make the difference between species coexistence and competitive exclusion. ATA influences may be an important new mechanism of coexistence.
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Affiliation(s)
- Pimsupa Jasmin Albert
- Department of Ecology and Evolutionary Biology and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Environmental Studies Program and Department of Biology, University of Oregon, Eugene, Oregon, USA
| | - Daniel C Reuman
- Department of Ecology and Evolutionary Biology and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
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Tang Y, Du E, Guo H, Wang Y, Peñuelas J, Reich PB. Rapid migration of Mongolian oak into the southern Asian boreal forest. Glob Chang Biol 2024; 30:e17002. [PMID: 37916481 DOI: 10.1111/gcb.17002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 09/06/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023]
Abstract
The migration of trees induced by climatic warming has been observed at many alpine treelines and boreal-tundra ecotones, but the migration of temperate trees into southern boreal forest remains less well documented. We conducted a field investigation across an ecotone of temperate and boreal forests in northern Greater Khingan Mountains of northeast China. Our analysis demonstrates that Mongolian oak (Quercus mongolica), an important temperate tree species, has migrated rapidly into southern boreal forest in synchrony with significant climatic warming over the past century. The average rate of migration is estimated to be 12.0 ± 1.0 km decade-1 , being slightly slower than the movement of isotherms (14.7 ± 6.4 km decade-1 ). The migration rate of Mongolian oak is the highest observed among migratory temperate trees (average rate 4.0 ± 1.0 km decade-1 ) and significantly higher than the rates of tree migration at boreal-tundra ecotones (0.9 ± 0.4 km decade-1 ) and alpine treelines (0.004 ± 0.003 km decade-1 ). Compared with the coexisting dominant boreal tree species, Dahurian larch (Larix gmelinii), temperate Mongolian oak is observed to have significantly lower capacity for light acquisition, comparable water-use efficiency but stronger capacity to utilize nutrients especially the most limiting nutrient, nitrogen. In the context of climatic warming, and in addition to a high seed dispersal capacity and potential thermal niche differences, the advantage of nutrient utilization, reflected by foliar elementomes and stable nitrogen isotope ratios, is also likely a key mechanism for Mongolian oak to coexist with Dahurian larch and facilitate its migration toward boreal forest. These findings highlight a rapid deborealization of southern Asian boreal forest in response to climatic warming.
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Affiliation(s)
- Yang Tang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Enzai Du
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Hongbo Guo
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Cerdanyola del Vallès, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Catalonia, Spain
| | - Peter B Reich
- Institute for Global Change Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Forest Resources, University of Minnesota, St. Paul, Minnesota, USA
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Zhang L, Huang X, Tong B, Chen M, Huang L, Liu J. Composition, functional, and niche differentiation of fungal communities in the rhizosphere and root endosphere of Cinnamomum migao in southwestern China. J Appl Microbiol 2023; 134:lxad239. [PMID: 37935485 DOI: 10.1093/jambio/lxad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/25/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
AIMS Roots are key parts of plant material circulation and energy flow, creating two distinct niches for the plant microbiome, such as the rhizosphere and root endosphere, which interact to maintain plant growth and health. In this study, two niches of plant rhizosphere and root endosphere were selected to study the composition and differences of fungi communities in order to better understand how differences in the structure and function of plant fungi communities affect plant health. METHODS AND RESULTS The community structure, diversity, and ecological function of fungi in the rhizosphere and root endosphere of Cinnamomum migao were studied using high-throughput sequencing techniques, traditional culture methods, and the FUNGuild database. The results of the analysis of alpha diversity showed that the diversity of rhizosphere fungal communities in C. migao was much higher than that of root endosphere communities. Some similarities and differences were noted between the two niche fungal communities, and some fungi had niche preferences. Functional prediction results demonstrated that fungi in the rhizosphere and root endosphere adopt multiple trophic modes, mostly saprophytic fungi. CONCLUSIONS This study provided a basis for an in-depth understanding of the structural variation, niche differentiation, and function of plant root-related fungal microbiota. We believe that it could provide guidance on the subsequent development of beneficial fungi.
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Affiliation(s)
- Lan Zhang
- Guizhou Academy of Forestry, Guiyang, Guizhou 550005, China
| | - Xiaolong Huang
- Guizhou Academy of Forestry, Guiyang, Guizhou 550005, China
| | - Bingli Tong
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Meng Chen
- Guizhou Academy of Forestry, Guiyang, Guizhou 550005, China
| | - Luting Huang
- Xiangzhong Normal College for Preschool Education, Shaoyang, Hunan 422099, China
| | - Jiming Liu
- College of Forestry, Guizhou University, Guiyang, Guizhou 550025, China
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Thieringer PH, Boyd ES, Templeton AS, Spear JR. Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman. Front Microbiol 2023; 14:1205558. [PMID: 37465028 PMCID: PMC10350532 DOI: 10.3389/fmicb.2023.1205558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H2 and CH4. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO2, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.
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Affiliation(s)
- Patrick H. Thieringer
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
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Agneray AC, Forister ML, Parchman TL, Leger EA. Does a history of population co-occurrence predict plant performance, community productivity, or invasion resistance? Ecology 2023:e4100. [PMID: 37165924 DOI: 10.1002/ecy.4100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/23/2023] [Accepted: 04/07/2023] [Indexed: 05/12/2023]
Abstract
A history of species co-occurrence in plant communities is hypothesized to lead to greater niche differentiation, more efficient resource partitioning, and more productive, resistant communities as a result of evolution in response to biotic interactions. A similar question can be asked of co-occurring populations: do individual species or community responses differ when communities are founded with plants sharing a history of population co-occurrence (sympatric) or originating from different locations (allopatric)? Using shrub, grass, and forb species from six locations in the western Great Basin, USA, we compared establishment, productivity, reproduction, phenology, and resistance to invaders for experimental communities with either sympatric or allopatric population associations. Each community type was planted with six taxa in outdoor mesocosms, measured over three growing seasons, and invaded with the annual grass Bromus tectorum in the final season. For most populations, the allopatric or sympatric status of neighbors was not important. However, in some cases it was beneficial for some species from some locations to be planted with allopatric neighbors, while others benefited from sympatric neighbors, and some of these responses had large effects. For instance, the Elymus population that benefited the most from allopatry grew 50% larger with allopatric neighbors than in single origin mesocosms. This response affected invasion resistance, as B. tectorum biomass was strongly affected by productivity and phenology of Elymus spp., as well as Poa secunda. Our results demonstrate that while community composition can affect plant performance in semi-arid plant communities, assembling communities from sympatric populations is not sufficient to ensure high productivity and invasion resistance. Instead, we observed an idiosyncratic interaction between sampling effects and evolutionary history, with the potential for seed source of individual populations to have community-level effects. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alison C Agneray
- Graduate Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Mail Stop 314, Reno, NV
- Bureau of Land Management Nevada State Office, 1340 Financial Boulevard, Reno, NV
| | - Matthew L Forister
- Graduate Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Mail Stop 314, Reno, NV
| | - Thomas L Parchman
- Graduate Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Mail Stop 314, Reno, NV
| | - Elizabeth A Leger
- Graduate Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Mail Stop 314, Reno, NV
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13
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Nie WB, Xie GJ, Tan X, Ding J, Lu Y, Chen Y, Yang C, He Q, Liu BF, Xing D, Ren N. Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation. Environ Sci Technol 2023; 57:7029-7040. [PMID: 37041123 DOI: 10.1021/acs.est.2c08094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been demonstrated to play important roles in the global methane and nitrogen cycle. However, despite diverse n-DAMO bacteria widely detected in environments, little is known about their physiology for microbial niche differentiation. Here, we show the microbial niche differentiation of n-DAMO bacteria through long-term reactor operations combining genome-centered omics and kinetic analysis. With the same inoculum dominated by both species "Candidatus Methylomirabilis oxyfera" and "Candidatus Methylomirabilis sinica", n-DAMO bacterial population was shifted to "Ca. M. oxyfera" in a reactor fed with low-strength nitrite, but shifted to "Ca. M. sinica" with high-strength nitrite. Metatranscriptomic analysis showed that "Ca. M. oxyfera" harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system for better uptake of nitrite, while "Ca. M. sinica" had a more active ion transport and stress response system, and more redundant function in nitrite reduction to mitigate nitrite inhibition. Importantly, the half-saturation constant of nitrite (0.057 mM vs 0.334 mM NO2-) and inhibition thresholds (0.932 mM vs 2.450 mM NO2-) for "Ca. M. oxyfera" vs "Ca. M. sinica", respectively, were highly consistent with genomic results. Integrating these findings demonstrated biochemical characteristics, especially the kinetics of nitrite affinity and inhibition determine niche differentiation of n-DAMO bacteria.
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Affiliation(s)
- Wen-Bo Nie
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yi Chen
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Chun Yang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Qiang He
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
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14
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Warnke L, Hertel D, Scheu S, Maraun M. Opening up new niche dimensions: The stoichiometry of soil microarthropods in European beech and Norway spruce forests. Ecol Evol 2023; 13:e10122. [PMID: 37223311 PMCID: PMC10202621 DOI: 10.1002/ece3.10122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/18/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
Niche theory fundamentally contributed to the understanding of animal diversity. However, in soil, the diversity of animals seems enigmatic since the soil is a rather homogeneous habitat, and soil animals are often generalist feeders. A new approach to understand soil animal diversity is the use of ecological stoichiometry. The elemental composition of animals may explain their occurrence, distribution, and density. This approach has been used before in soil macrofauna, but this study is the first to investigate soil mesofauna. Using inductively coupled plasma optic emission spectrometry (ICP-OES), we analyzed the concentration of a wide range of elements (Al, Ca, Cu, Fe, K, Mg, Mn, Na, P, S, Zn) in 15 soil mite taxa (Oribatida, Mesostigmata) from the litter of two different forest types (beech, spruce) in Central Europe (Germany). Additionally, the concentration of carbon and nitrogen, and their stable isotope ratios (15N/14N, 13C/12C), reflecting their trophic niche, were measured. We hypothesized that (1) stoichiometry differs between mite taxa, (2) stoichiometry of mite taxa occurring in both forest types is not different, and (3) element composition is correlated to trophic level as indicated by 15N/14N ratios. The results showed that stoichiometric niches of soil mite taxa differed considerably indicating that elemental composition is an important niche dimension of soil animal taxa. Further, stoichiometric niches of the studied taxa did not differ significantly between the two forest types. Calcium was negatively correlated with trophic level indicating that taxa incorporating calcium carbonate in their cuticle for defense occupy lower trophic positions in the food web. Furthermore, a positive correlation of phosphorus with trophic level indicated that taxa higher in the food web have higher energetic demand. Overall, the results indicate that ecological stoichiometry of soil animals is a promising tool for understanding their diversity and functioning.
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Affiliation(s)
- Lara Warnke
- JFB Institute of Zoology and AnthropologyUniversity of GöttingenGöttingenGermany
| | - Dietrich Hertel
- Albrecht von Haller Institute for Plant Sciences, Plant Ecology and Ecosystems ResearchUniversity of GöttingenGöttingenGermany
| | - Stefan Scheu
- JFB Institute of Zoology and AnthropologyUniversity of GöttingenGöttingenGermany
- Centre of Biodiversity and Sustainable Land UseUniversity of GöttingenGöttingenGermany
| | - Mark Maraun
- JFB Institute of Zoology and AnthropologyUniversity of GöttingenGöttingenGermany
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15
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Li D, Zhang C, Cao Y, Gao M, Chang S, Xu M, Jin Z, Ni H. Food preference strategy of four sympatric rodents in a temperate forest in northeast China. Zookeys 2023; 1158:163-177. [PMID: 37234253 PMCID: PMC10208086 DOI: 10.3897/zookeys.1158.96886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/13/2023] [Indexed: 05/27/2023] Open
Abstract
Rodents are well known as both seed predators and dispersers of various plant species in forest ecosystems, and they play an important role in the regeneration of vegetation. Thus, the research on seed selection and vegetation regeneration by sympatric rodents is an interesting topic. To understand the characteristics of preferences of rodents for different seeds, a semi-natural enclosure experiment was performed with four rodent species (Apodemuspeninsulae, Apodemusagrarius, Tscherskiatriton, and Clethrionomysrufocanus) and the seeds of seven plant species (Pinuskoraiensis, Corylusmandshurica, Quercusmongolica, Juglansmandshurica, Armeniacasibirica, Prunussalicina, and Cerasustomentosa) to investigate the differentiation in niches and patterns of resource utilization of sympatric rodents. The results showed that all the rodents had consumed many seeds of Pi.koraiensis, Co.mandshurica, and Q.mongolica but differed significantly in how they selected the different seeds. The rate of utilization (Ri) of Pi.koraiensis, Co.mandshurica, and Q.mongolica exhibited the highest values. The Ei values indicated that the rodents tested exhibited differences in their priorities used to select the seeds from different plant species. All four species of rodents exhibited obvious preferences for certain seeds. Korean field mice preferentially consumed the seeds of Q.mongolica, Co.mandshurica, and Pi.koraiensis. Striped field mice favor the seeds of Co.mandshurica, Q.mongolica, P.koraiensis, and Nanking cherry. Greater long-tailed hamsters prefer to consume the seeds of Pi.koraiensis, Co.mandshurica, Q.mongolica, Pr.salicina, and Ce.tomentosa. Clethrionomysrufocanus likes to eat the seeds of Pi.koraiensis, Q.mongolica, Co.mandshurica, and Ce.tomentosa. The results supported our hypothesis that sympatric rodents overlap in food selection. However, each rodent species has a marked preference for food selection, and different rodent species differ in their food preferences. This reflects the role of distinct food niche differentiation in their coexistence.
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Affiliation(s)
- Dianwei Li
- Heilongjiang Academy of Forestry, No. 134 Haping Road, Harbin, Heilongjiang 150081, ChinaHeilongjiang Academy of ForestryHarbinChina
- College of Life Sciences and Technology, Mudanjiang Normal University, No. 191 Wenhua Road, Mudanjiang, Heilongjiang 157011, ChinaMudanjiang Normal UniversityMudanjiangChina
- College of Wildlife and Protected Area, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, ChinaNortheast Forestry UniversityHarbinChina
| | - Chengzhi Zhang
- College of Life Sciences and Technology, Mudanjiang Normal University, No. 191 Wenhua Road, Mudanjiang, Heilongjiang 157011, ChinaMudanjiang Normal UniversityMudanjiangChina
| | - Yuwei Cao
- College of Life Sciences and Technology, Mudanjiang Normal University, No. 191 Wenhua Road, Mudanjiang, Heilongjiang 157011, ChinaMudanjiang Normal UniversityMudanjiangChina
| | - Ming Gao
- College of Life Sciences and Technology, Mudanjiang Normal University, No. 191 Wenhua Road, Mudanjiang, Heilongjiang 157011, ChinaMudanjiang Normal UniversityMudanjiangChina
| | - Shiqi Chang
- College of Life Sciences and Technology, Mudanjiang Normal University, No. 191 Wenhua Road, Mudanjiang, Heilongjiang 157011, ChinaMudanjiang Normal UniversityMudanjiangChina
| | - Menghao Xu
- College of Life Sciences and Technology, Mudanjiang Normal University, No. 191 Wenhua Road, Mudanjiang, Heilongjiang 157011, ChinaMudanjiang Normal UniversityMudanjiangChina
| | - Zhimin Jin
- College of Life Sciences and Technology, Mudanjiang Normal University, No. 191 Wenhua Road, Mudanjiang, Heilongjiang 157011, ChinaMudanjiang Normal UniversityMudanjiangChina
| | - Hongwei Ni
- Heilongjiang Academy of Forestry, No. 134 Haping Road, Harbin, Heilongjiang 150081, ChinaHeilongjiang Academy of ForestryHarbinChina
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16
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Keuter S, Koch H, Nowka B, Lipski A, Kruse M, Lücker S, Spieck E. A novel Nitrospira lineage isolated from activated sludge using elevated temperatures. FEMS Microbiol Lett 2023; 370:7134069. [PMID: 37081766 DOI: 10.1093/femsle/fnad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 04/22/2023] Open
Abstract
The genus Nitrospira represents the dominant nitrite-oxidizing clade in most wastewater treatment plants (WWTPs) globally, and several Nitrospira strains have been isolated from activated sludge. Using a pre-enrichment strategy with alternating nitrifying and denitrifying conditions, followed by incubation at elevated temperatures, we isolated a novel Nitrospira species, named Nitrospira tepida. This moderately thermophilic species with optimal growth between 37 and 45°C is only distantly related to other Nitrospira and forms a novel lineage VII within the genus, together with few environmental 16S rRNA gene sequences predominantly detected in thermal wastewater or oxygen-limited systems. Genomic and physiological analyses revealed remarkable differences between N. tepida and two other isolates previously obtained from the same WWTP, suggesting niche differentiation between these nitrite oxidizers. N. tepida grows in aggregates, and tolerates nitrite and nitrate concentrations of up to 20 mM and 40 mM, respectively. The Km value for nitrite of N. tepida is 77 ± 26 µM. In summary, this novel Nitrospira lineage seems to be well adapted for wastewater treatment processes at elevated temperatures and limited aeration, conditions that potentially reduce operational costs of such systems.
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Affiliation(s)
- Sabine Keuter
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Hanna Koch
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Boris Nowka
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - André Lipski
- Department of Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Myriam Kruse
- Department of Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Eva Spieck
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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17
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Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat complexity affects microbial growth in fractal maze. Curr Biol 2023; 33:1448-1458.e4. [PMID: 36933553 DOI: 10.1016/j.cub.2023.02.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/19/2023]
Abstract
The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.
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Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Sölvegatan 16, 223 63 Lund, Sweden
| | - Edith C Hammer
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden; Centre for Environmental and Climate Science, CEC, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
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18
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Liu Q, Turlings TCJ, Li Y. Can herbivores sharing the same host plant be mutualists? Trends Ecol Evol 2023; 38:509-511. [PMID: 36863968 DOI: 10.1016/j.tree.2023.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 03/04/2023]
Abstract
Resource partitioning is considered to be a prerequisite for coexisting species to evolve from competition to mutualism. This is uniquely different for two major pest insects of rice. These herbivores preferentially opt to coinfest the same host plants, and through plant-mediated mechanisms, cooperatively utilize these plants in a mutualistic manner.
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Affiliation(s)
- Qingsong Liu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences and College of Agriculture, Henan University, Kaifeng 475004, China
| | - Ted C J Turlings
- Laboratory of Fundamental and Applied Research in Chemical Ecology, University of Neuchâtel, Neuchâtel 2000, Switzerland
| | - Yunhe Li
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences and College of Agriculture, Henan University, Kaifeng 475004, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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19
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Uiterwaal SF, Squires AJ, Grappone BA, Dillard B, Castaneda A, Kim SL, DeLong JP. Intraguild predation is increased in areas of low prey diversity in a generalist predator community. J Anim Ecol 2023; 92:901-912. [PMID: 36779228 DOI: 10.1111/1365-2656.13901] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/02/2023] [Indexed: 02/14/2023]
Abstract
Niche differentiation and intraguild predation (IGP) can allow ecologically similar species to coexist, although it is unclear which coexistence mechanism predominates in consumer communities. Until now, a limited ability to quantify diets from metabarcoding data has precluded the use of sequencing data to determine the relative importance of these mechanisms. Here, we pair a recent metabarcoding quantification approach with stable isotope analysis to examine diet composition in a wolf spider community. We compare the prevalence of resource partitioning and IGP in these spiders and test whether factors that influence foraging performance, including individual identity, morphology, prey community and environmental conditions, can explain variation in diet composition and IGP. Extensive IGP is likely the primary coexistence mechanism in this community, and other factors to which foraging variation is often attributed do not explain diet composition and IGP here. Rather, IGP increases as prey diversity decreases. Foragers are driven to IGP where resource niches are limited. We highlight the need to examine how drivers of predator-prey interaction strengths translate into foraging in natural systems.
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Affiliation(s)
- Stella F Uiterwaal
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Amber J Squires
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Bennett A Grappone
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Brian Dillard
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Ariadne Castaneda
- Department of Life and Environmental Sciences, University of California, Merced, California, USA
| | - Sora L Kim
- Department of Life and Environmental Sciences, University of California, Merced, California, USA
| | - John P DeLong
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
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20
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Cheng X, Xiang X, Yun Y, Wang W, Wang H, Bodelier PLE. Archaea and their interactions with bacteria in a karst ecosystem. Front Microbiol 2023; 14:1068595. [PMID: 36814573 PMCID: PMC9939782 DOI: 10.3389/fmicb.2023.1068595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 + availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca2+, and NO2 -. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,College of Life Science, Shangrao Normal University, Shangrao, China
| | - Yuan Yun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,College of Life Sciences, Nankai University, Tianjin, China
| | - Weiqi Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Hongmei Wang, ✉ ; ✉
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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21
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Wang Y, Zeng X, Ma Q, Zhang Y, Yu W, Zheng Z, Zhang N, Xu L. Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China. Front Microbiol 2023; 14:1095937. [PMID: 36819044 PMCID: PMC9929954 DOI: 10.3389/fmicb.2023.1095937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0-20 cm, topsoil; 20-40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH4 +-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH4 +-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems.
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Affiliation(s)
- Yanan Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Xibai Zeng, ✉
| | - Qiang Ma
- Insitute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yang Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wantai Yu
- Insitute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhong Zheng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liyang Xu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Herzog SA, Latvis M. Community‐level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in the northern Great Plains. Ecol Evol 2022; 12:e9453. [PMID: 36340814 PMCID: PMC9627050 DOI: 10.1002/ece3.9453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022] Open
Abstract
Niche differentiation has served as one explanation for species coexistence, and phylogenetic relatedness provides a means to approximate how ecologically similar species are to each other. To explore the contribution of rare species to community phylogenetic diversity, we sampled 21 plant communities across the Prairie Coteau ecoregion, an area of high conservation concern. We used breakpoint analysis through the iterative addition of less abundant species to the phylogenetic tree for each community to assess the contribution of rare species to community phylogenetic diversity. We also quantify the phylogenetic signal of abundance using Blomberg's K statistic and calculated the phylogenetic similarity between rare and common species using a phylogenetic beta‐diversity metric (Dnn). To estimate the phylogenetic structuring of these prairie communities, we calculated two common metrics that capture evolutionary relatedness at different scales (MPD and MNTD). Additionally, we examine the correlation between Faith's PD, MPD, and MNTD and species richness. We found rare species do not generally contribute higher levels of phylogenetic diversity than common species. Eight communities had significant breakpoints, with only four communities having an increasing trend for the rarest species. The phylogenetic signal for abundance was low but significant in only four communities, and communities had lower phylogenetic diversity than expected from the regional species pool. Finally, the strength of the correlation between species richness and phylogenetic diversity was mixed. Our results indicate niche differentiation does not explain the persistence of rare species in tallgrass prairies, as they were more closely related than expected from random, suggesting high functional redundancy between rare and common species. This is promising for the long‐term resilience of this ecosystem, but only insofar as enough species remain in the system. With ongoing biodiversity loss, it is essential that we understand the role rare species play in their communities.
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Affiliation(s)
- Sarah A. Herzog
- Department of Natural Resource ManagementSouth Dakota State UniversityBrookingsSouth DakotaUSA,C.A. Taylor HerbariumSouth Dakota State UniversityBrookingsSouth DakotaUSA,Division of BiologyKansas State UniversityManhattanKansasUSA
| | - Maribeth Latvis
- Department of Natural Resource ManagementSouth Dakota State UniversityBrookingsSouth DakotaUSA,C.A. Taylor HerbariumSouth Dakota State UniversityBrookingsSouth DakotaUSA
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23
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Liu L, Ma L, Feng J, Lu X. Dynamic Fluctuation and Niche Differentiation of Fungal Pathogens Infecting Bell Pepper Plants. Appl Environ Microbiol 2022; 88:e0100322. [PMID: 36036572 DOI: 10.1128/aem.01003-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plant microbiome is shaped by plant development and microbial interaction. Fungal pathogens infecting bell pepper plants may fluctuate across the growing seasons. Dynamic fluctuation of the microbiome and fungal pathogens in bell pepper plants is poorly understood, and the origin of fungal pathogens causing fruit rot and leaf wilt has been barely investigated. In this study, we used amplicon sequencing (i.e., 16S rRNA and internal transcribed spacer [ITS] sequencing) to explore the compositional variations of the microbiome in bell pepper plants and studied the fluctuation of fungal pathogens across the growing seasons. Co-occurrence network analysis was applied to track the origin and dissemination route of fungal pathogens that infected bell pepper plants. ITS and 16S rRNA sequencing analyses demonstrated that fungal pathogens infecting fruits and leaves probably belonged to the Penicillium, Cladosporium, Fusarium, and unclassified_Sclerotiniaceae genera rather than one specific genus. The dominant fungal pathogens were different, along with the development of bell pepper plants. Both plant development and fungal pathogens shaped microbial communities in bell pepper plants across the growing seasons. Fungal pathogens decreased species richness and diversity of fungal communities in fungus-infected fruit and leaf tissues but not the uninfected stem tissues. Bacterial metabolic functions of xenobiotics increased in fungus-infected leaves at a mature developmental stage. Competitive interaction was present between fungal and bacterial communities in leaves. Co-occurrence network analysis revealed that the origins of fungal pathogens included the greenhouse, packing house, and storage room. Niche differentiation of microbes was discovered among these locations. IMPORTANCE Bell peppers are widely consumed worldwide. Fungal pathogen infections of bell peppers lead to enormous economic loss. To control fungal pathogens and increase economic benefit, it is essential to investigate the shifting patterns of the microbiome and fungal pathogens in bell pepper plants across the growing seasons. In this study, bell pepper plant diseases observed in fruits and leaves were caused by different fungal pathogens. Fungal pathogens originated from the greenhouse, packing house, and storage room, and niche differentiation existed among microbes. This study improves the understanding of dynamic fluctuation and source of fungal pathogens infecting bell pepper plants in the farming system. It also facilitates precise management of fungal pathogens in the greenhouse.
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24
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Garvey PM, Glen AS, Clout MN, Nichols M, Pech RP. Niche partitioning in a guild of invasive mammalian predators. Ecol Appl 2022; 32:e2566. [PMID: 35138656 PMCID: PMC9285952 DOI: 10.1002/eap.2566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 05/28/2023]
Abstract
Predators compete aggressively for resources, establishing trophic hierarchies that influence ecosystem structure. Competitive interactions are particularly important in invaded ecosystems where introduced predators can suppress native prey species. We investigated whether niche partitioning exists within a guild of invasive mammalian predators and determined the consequences for native species. Over 4405 camera-trap days, we assessed interactions among three invasive predators: two apex predators (feral cats Felis catus and ferrets Mustela furo) and a mesopredator (stoats Mustela erminea), in relation to their primary prey (lagomorphs, rodents and birds) and habitat use. Further, we tested for mesopredator release by selectively removing cats and ferrets in a pulse perturbation experiment. We found compelling evidence of niche partitioning; spatiotemporal activity of apex predators maximized access to abundant invasive prey, with ferrets targeting lagomorphs and cats targeting rodents. Mesopredators adjusted their behavior to reduce the risk of interference competition, thereby restricting access to abundant prey but increasing predation pressure on diurnal native birds. Stoats were only recorded at the treatment site after both larger predators were removed, becoming the most frequently detected predator at 6 months post-perturbation. We suggest there is spatial and resource partitioning within the invasive predator guild, but that this is incomplete, and avoidance is achieved by temporal partitioning within overlapping areas. Niche partitioning among invasive predators facilitates coexistence, but simultaneously intensifies predation pressure on vulnerable native species.
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Affiliation(s)
| | | | - Mick N. Clout
- Centre for Biodiversity and Biosecurity, School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Margaret Nichols
- Centre for Wildlife Management and ConservationLincoln UniversityCanterburyNew Zealand
| | - Roger P. Pech
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
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25
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White H, Vos M, Sheppard SK, Pascoe B, Raymond B. Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades. Mol Ecol 2022; 31:3584-3597. [PMID: 35510788 PMCID: PMC9324797 DOI: 10.1111/mec.16490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/31/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
Bacterial clades are often ecologically distinct, despite extensive horizontal gene transfer (HGT). How selection works on different parts of bacterial pan‐genomes to drive and maintain the emergence of clades is unclear. Focusing on the three largest clades in the diverse and well‐studied Bacillus cereus sensu lato group, we identified clade‐specific core genes (present in all clade members) and then used clade‐specific allelic diversity to identify genes under purifying and diversifying selection. Clade‐specific accessory genes (present in a subset of strains within a clade) were characterized as being under selection using presence/absence in specific clades. Gene ontology analyses of genes under selection revealed that different gene functions were enriched in different clades. Furthermore, some gene functions were enriched only amongst clade‐specific core or accessory genomes. Genes under purifying selection were often clade‐specific, while genes under diversifying selection showed signs of frequent HGT. These patterns are consistent with different selection pressures acting on both the core and the accessory genomes of different clades and can lead to ecological divergence in both cases. Examining variation in allelic diversity allows us to uncover genes under clade‐specific selection, allowing ready identification of strains and their ecological niche.
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Affiliation(s)
- Hugh White
- Centre for Ecology and Conservation, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
| | - Samuel K Sheppard
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - Ben Pascoe
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - Ben Raymond
- Centre for Ecology and Conservation, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
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26
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Okamoto S, Takenaka M, Tojo K. Seasonal modifications of longitudinal distribution patterns within a stream: Interspecific interactions in the niche overlap zones of two Ephemera mayflies. Ecol Evol 2022; 12:e8766. [PMID: 35386869 PMCID: PMC8975782 DOI: 10.1002/ece3.8766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/07/2022] Open
Abstract
Niche differentiation between closely related species leads to differentiation of their habitats. Segregation based on slight differences in environmental factors, that is niche differentiation on the microhabitat scale, allows more species to inhabit a certain geographic space. Therefore, such fine scale niche differentiation is an important factor in the support of species diversity. In addition, niche differentiation on the microhabitat scale and/or the differentiation of breeding seasons can be considered typical mechanisms that facilitate multispecies' co-existence. In this study, sister species (Commonly, Ephemera japonica inhabit at upstream region and Ephemera strigata inhabit at middle stream region), which often coexist in the upper to middle reaches of river systems of the Japanese Islands, were targeted and the following aspects were investigated. First, differences in habitat preference and interspecific differences in flow distribution patterns on a geographically fine scale were tracked in detail. Subsequently, the temporal transitions of their distribution patterns were investigated in detail and seasonal changes were investigated. Finally, we thoroughly investigated the disappearance of nymphs of each species from the river due to emergence affected the distribution of each species (by conducting daily emergence surveys). Combining results of these multiple studies also suggested that there may be spatiotemporal interspecial interaction between these two species within/around their overlapping regions. Traditionally, the longitudinal distribution pattern of these two Ephemera mayflies has been thought to be established based on a difference in habitat preferences, but this study revealed that the interspecific interaction between the two species also plays an important role. This study provides new insights into species diversity and distribution pattern formation in river-dwelling species.
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Affiliation(s)
- Seiya Okamoto
- Division of Mountain and Environmental ScienceInterdisciplinary Graduate School of Science and TechnologyShinshu UniversityMatsumotoJapan
| | - Masaki Takenaka
- Sugadaira Research StationMountain Science CenterUniversity of TsukubaUedaJapan
- Department of BiologyFaculty of ScienceShinshu UniversityMatsumotoJapan
| | - Koji Tojo
- Division of Mountain and Environmental ScienceInterdisciplinary Graduate School of Science and TechnologyShinshu UniversityMatsumotoJapan
- Department of BiologyFaculty of ScienceShinshu UniversityMatsumotoJapan
- Institute of Mountain ScienceShinshu UniversityMatsumotoJapan
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27
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Wu W, Wang X, Ren Z, Zhou X, Du G. N-Induced Species Loss Dampened by Clipping Mainly Through Suppressing Dominant Species in an Alpine Meadow. Front Plant Sci 2022; 13:815011. [PMID: 35392523 PMCID: PMC8980528 DOI: 10.3389/fpls.2022.815011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen addition and clipping can exert substantial impact on species diversity but their interactions and the underlying mechanisms still remain unclear. Resource competition theory holds that sufficiently strong competitive ability of dominant species can lead to the losses of subordinate species through competitive exclusion, while niche differentiation theory suggests that the persistence of subordinate species in competitive systems can be promoted by guaranteeing positive growth rates of rare species. Taking advantage of a field experiment with nitrogen addition (10 g N m-2 year-1) and different clipping intensities (2, 15, and 30 cm) treatments in a Tibetan alpine meadow across 2015-2020, we assessed the relative importance of competitively dominant species and niche differentiation in driving species diversity changes via using community weighted mean (CWM) and variation coefficient of nearest neighbor distance (CV_NND) of functional traits including height, specific leaf area (SLA) and leaf dry matter content (LDMC). We show that nitrogen enrichment drove a strong plant diversity loss (P < 0.001). Clipping at different intensities had little effect on species diversity, but it can reduce the N-induced diversity loss. Nitrogen addition and clipping caused changes in community diversity were mainly indirectly attributed to their effects on community functional composition, and the competitive ability of dominant species. Nitrogen increased the CWM of functional traits to improve the competitive ability of dominant species. In contrast, clipping influenced species diversity positively by decreasing CWMheight (P < 0.001), and also negatively by increasing CWMSLA (P < 0.001) and decreasing CV_NNDSLA (P < 0.05). Interacting with N addition, clipping resulted in a neutral effect on species diversity, because clipping could offset the negative effects of nitrogen addition through an opposite effect on CWMheight. This study provides new insights into the mechanisms of diversity maintenance with respect to nitrogen addition and clipping. Thus, clipping is recommended as a useful management strategy to alleviate the species loss caused by nutrients enrichment and maintain the diversity of grassland ecosystems.
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28
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Ren L, Jensen K, Porada P, Mueller P. Biota-mediated carbon cycling-A synthesis of biotic-interaction controls on blue carbon. Ecol Lett 2022; 25:521-540. [PMID: 35006633 DOI: 10.1111/ele.13940] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023]
Abstract
Research into biotic interactions has been a core theme of ecology for over a century. However, despite the obvious role that biota play in the global carbon cycle, the effects of biotic interactions on carbon pools and fluxes are poorly understood. Here we develop a conceptual framework that illustrates the importance of biotic interactions in regulating carbon cycling based on a literature review and a quantitative synthesis by means of meta-analysis. Our study focuses on blue carbon ecosystems-vegetated coastal ecosystems that function as the most effective long-term CO2 sinks of the biosphere. We demonstrate that a multitude of mutualistic, competitive and consumer-resource interactions between plants, animals and microbiota exert strong effects on carbon cycling across various spatial scales ranging from the rhizosphere to the landscape scale. Climate change-sensitive abiotic factors modulate the strength of biotic-interaction effects on carbon fluxes, suggesting that the importance of biota-mediated carbon cycling will change under future climatic conditions. Strong effects of biotic interactions on carbon cycling imply that biosphere-climate feedbacks may not be sufficiently represented in current Earth system models. Inclusion of new functional groups in these models, and new approaches to simplify species interactions, may thus improve the predictions of biotic effects on the global climate.
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Affiliation(s)
- Linjing Ren
- Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany.,State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, P. R. China
| | - Kai Jensen
- Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Philipp Porada
- Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Peter Mueller
- Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany.,Smithsonian Environmental Research Center, Edgewater, Maryland, USA
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29
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Luo W, Ni M, Wang Y, Lan R, Eissenstat DM, Cahill JF, Li B, Chu C. Limited evidence of vertical fine-root segregation in a subtropical forest. New Phytol 2021; 231:2308-2318. [PMID: 34110016 DOI: 10.1111/nph.17546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Vertical root segregation and the resulting niche partitioning can be a key underpinning of species coexistence. This could result from substantial interspecific variations in root profiles and rooting plasticity in response to soil heterogeneity and neighbours, but they remain largely untested in forest communities. In a diverse forest in subtropical China, we randomly sampled > 4000 root samples from 625 0-30 cm soil profiles. Using morphological and DNA-based methods, we identified 109 woody plant species, determined the degree of vertical fine-root segregation, and examined rooting plasticity in response to soil heterogeneity and neighbour structure. We found no evidence of vertical fine-root segregation among cooccurring species. By contrast, root abundance of different species tended to be positively correlated within soil zones. Underlying these findings was a lack of interspecific variation in fine-root profiles with over 90% of species concentrated in the 0-10 cm soil zone with only one species dominating in the 10-20 cm soil zone. Root profiles exhibited low responsiveness to root neighbours but tended to be shallow in soils with low phosphorus and copper content. These findings suggest that if there is niche differentiation leading to coexistence in this diverse forest, it would be occurring by mechanisms other than vertical fine-root segregation.
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Affiliation(s)
- Wenqi Luo
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ming Ni
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Youshi Wang
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Runxuan Lan
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - David M Eissenstat
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Buhang Li
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
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30
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Kim H, Lee YH. Spatiotemporal Assembly of Bacterial and Fungal Communities of Seed-Seedling-Adult in Rice. Front Microbiol 2021; 12:708475. [PMID: 34421867 PMCID: PMC8375405 DOI: 10.3389/fmicb.2021.708475] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/19/2021] [Indexed: 01/04/2023] Open
Abstract
Seeds harbor not only genetic information about plants but also microbial communities affecting plants’ vigor. Knowledge on the movement and formation of seed microbial communities during plant development remains insufficient. Here, we address this knowledge gap by investigating endophytic bacterial and fungal communities of seeds, seedlings, and adult rice plants. We found that seed coats act as microbial niches for seed bacterial and fungal communities. The presence or absence of the seed coat affected taxonomic composition and diversity of bacterial and fungal communities associated with seeds and seedlings. Ordination analysis showed that niche differentiation between above- and belowground compartments leads to compositional differences in endophytic bacterial and fungal communities originating from seeds. Longitudinal tracking of the composition of microbial communities from field-grown rice revealed that bacterial and fungal communities originating from seeds persist in the leaf, stem, and root endospheres throughout the life cycle. Our study provides ecological insights into the assembly of the initial endophytic microbial communities of plants from seeds.
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Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea.,Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.,Plant Immunity Research Center, Seoul National University, Seoul, South Korea
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31
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Dietschler NJ, Bittner TD, Trotter RT, Fahey TJ, Whitmore MC. Biological Control of Hemlock Woolly Adelgid: Implications of Adult Emergence Patterns of Two Leucopis spp. (Diptera: Chamaemyiidae) and Laricobius nigrinus (Coleoptera: Derodontidae) Larval Drop. Environ Entomol 2021; 50:803-813. [PMID: 33942871 DOI: 10.1093/ee/nvab037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The hemlock woolly adelgid (Hemiptera: Adelgidae Adelges tsugae Annand) poses a serious threat to hemlocks in eastern North America, and ongoing research is focused on the identification and development of biological controls to protect and manage hemlock resources. Three predators native to the Pacific Northwest of North America that have been the focus of much research are Leucopis argenticollis (Zetterstedt), Leucopis piniperda (Malloch) (Diptera: Chamaemyiidae), and Laricobius nigrinus (Fender) (Coleoptera: Derodontidae). This study addresses the knowledge gap of adult Leucopis spp. emergence patterns, with comparisons to the timing of larval La. nigrinus drop for pupation. Adult Leucopis spp. emergence was observed in the lab from field-collected, adelgid-infested foliage from Washington state in 2019 and 2020. Adult Leucopis spp. were collected daily as they emerged from foliage collections and identified to species using morphological features; a subset was validated using DNA barcoding. Accumulated heating degree days were calculated to compare a standardized emergence timing across collections made at different locations and temperature regimes. The abundance of the two Leucopis spp. and of the combined Leucopis spp. and La. nigrinus varied among sites and years, and no species was consistently more abundant than the other. Evaluations of seasonal emergence trends of the three species determine the predator complex behaves in a temporally stratified and predictable way. Emergence of adult Le. argenticollis was observed first, followed by La. nigrinus larval drop, with Le. piniperda emerging at the end of larval drop, and finally a second emergence of Le. argenticollis.
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Affiliation(s)
- Nicholas J Dietschler
- Department of Natural Resources and the Environment, Cornell University, 111 Fernow Hall, Tower Road, Ithaca, NY 14853, USA
| | - Tonya D Bittner
- Department of Natural Resources and the Environment, Cornell University, 111 Fernow Hall, Tower Road, Ithaca, NY 14853, USA
| | - R Talbot Trotter
- USDA Forest Service, Northern Research Station, 51 Mill Pond Road, Hamden, CT 06514, USA
| | - Timothy J Fahey
- Department of Natural Resources and the Environment, Cornell University, 111 Fernow Hall, Tower Road, Ithaca, NY 14853, USA
| | - Mark C Whitmore
- Department of Natural Resources and the Environment, Cornell University, 111 Fernow Hall, Tower Road, Ithaca, NY 14853, USA
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32
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Maltseva AL, Varfolomeeva MA, Ayanka RV, Gafarova ER, Repkin EA, Pavlova PA, Shavarda AL, Mikhailova NA, Granovitch AI. Linking ecology, morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus Littorina ( Neritrema). Ecol Evol 2021; 11:11134-11154. [PMID: 34429908 PMCID: PMC8366845 DOI: 10.1002/ece3.7901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/08/2021] [Accepted: 06/22/2021] [Indexed: 12/03/2022] Open
Abstract
Divergence of ecological niches in phylogenetically closely related species indicates the importance of ecology in speciation, especially for sympatric species are considered. Such ecological diversification provides an advantage of alleviating interspecies competition and promotes more efficient exploitation of environmental resources, thus being a basis for ecological speciation. We analyzed a group of closely related species from the subgenus Neritrema (genus Littorina, Caenogastropoda) from the gravel-bouldery shores. In two distant sites at the Barents and Norwegian Sea, we examined the patterns of snail distribution during low tide (quantitative sampling stratified by intertidal level, presence of macrophytes, macrophyte species, and position on them), shell shape and its variability (geometric morphometrics), and metabolic characteristics (metabolomic profiling). The studied species diversified microbiotopes, which imply an important role of ecological specification in the recent evolution of this group. The only exception to this trend was the species pair L. arcana / L. saxatilis, which is specifically discussed. The ecological divergence was accompanied by differences in shell shape and metabolomic characteristics. Significant differences were found between L. obtusata versus L. fabalis and L. saxatilis / L. arcana versus L. compressa both in shell morphology and in metabolomes. L. saxatilis demonstrated a clear variability depending on intertidal level which corresponds to a shift in conditions within the occupied microhabitat. Interestingly, the differences between L. arcana (inhabiting the upper intertidal level) and L. compressa (inhabiting the lower one) were analogous to those between the upper and lower fractions of L. saxatilis. No significant level-dependent changes were found between the upper and lower fractions of L. obtusata, most probably due to habitat amelioration by fucoid macroalgae. All these results are discussed in the contexts of the role of ecology in speciation, ecological niche dynamics and conservatism, and evolutionary history of the Neritrema species.
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Affiliation(s)
- Arina L Maltseva
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Marina A Varfolomeeva
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Roman V Ayanka
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Elizaveta R Gafarova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Egor A Repkin
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Polina A Pavlova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Alexei L Shavarda
- Department of Analytical Phytochemistry Komarov Botanical Institute St. Petersburg Russia
- Research Park Centre for Molecular and Cell Technologies St. Petersburg State University St. Petersburg Russia
| | - Natalia A Mikhailova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
- Centre of Cell Technologies Institute of Cytology Russian Academy of Sciences St. Petersburg Russia
| | - Andrei I Granovitch
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
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33
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Wang JT, Shen JP, Zhang LM, Singh BK, Delgado-Baquerizo M, Hu HW, Han LL, Wei WX, Fang YT, He JZ. Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems. Front Microbiol 2021; 12:678290. [PMID: 34305842 PMCID: PMC8299105 DOI: 10.3389/fmicb.2021.678290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/17/2021] [Indexed: 12/05/2022] Open
Abstract
Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.
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Affiliation(s)
- Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Ju-Pei 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
| | - Li-Mei Zhang
- 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
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, United States
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wen-Xue Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yun-Ting Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
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Gross N, Le Bagousse-Pinguet Y, Liancourt P, Saiz H, Violle C, Munoz F. Unveiling ecological assembly rules from commonalities in trait distributions. Ecol Lett 2021; 24:1668-1680. [PMID: 34128304 DOI: 10.1111/ele.13789] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/02/2020] [Accepted: 05/03/2021] [Indexed: 11/30/2022]
Abstract
Deciphering the effect of neutral and deterministic processes on community assembly is critical to understand and predict diversity patterns. The information held in community trait distributions is commonly assumed as a signature of these processes, but empirical and modelling attempts have most often failed to untangle their confounding, sometimes opposing, impacts. Here, we simulated the assembly of trait distributions through stochastic (dispersal limitation) and/or deterministic scenarios (environmental filtering and niche differentiation). We characterized the shape of trait distributions using the skewness-kurtosis relationship. We identified commonalities in the co-variation between the skewness and the kurtosis of trait distributions with a unique signature for each simulated assembly scenario. Our findings were robust to variation in the composition of regional species pools, dispersal limitation and environmental conditions. While ecological communities can exhibit a high degree of idiosyncrasy, identification of commonalities across multiple communities can help to unveil ecological assembly rules in real-world ecosystems.
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Affiliation(s)
- Nicolas Gross
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Ecosystème Prairial, Clermont-Ferrand, France
| | | | - Pierre Liancourt
- Institute of Botany of the Czech Academy of Science, Průhonice, Czech Republic.,Plant Ecology Group, University of Tübingen, Tübingen, Germany
| | - Hugo Saiz
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Cyrille Violle
- CEFE, Univ Montpellier - CNRS - EPHE - IRD - Univ Paul Valéry Montpellier, Montpellier Cedex 5, France
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35
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Lei F, Liu X, Huang H, Fu S, Zou K, Zhang S, Zhou L, Zeng J, Liu H, Jiang L, Miao B, Liang Y. The Macleaya cordata Symbiont: Revealing the Effects of Plant Niches and Alkaloids on the Bacterial Community. Front Microbiol 2021; 12:681210. [PMID: 34177865 PMCID: PMC8219869 DOI: 10.3389/fmicb.2021.681210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Endophytes are highly associated with plant growth and health. Exploring the variation of bacterial communities in different plant niches is essential for understanding microbe-plant interactions. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from the rhizospheric soil and different parts of the Macleaya cordata. The results indicated that the bacterial community structure varied widely among compartments. Bacterial diversity was observed to be the highest in the rhizospheric soil and the lowest in fruits. Proteobacteria, Actinobacteria, and Bacteroidetes were found as the dominant phyla. The genera Sphingomonas (∼47.77%) and Methylobacterium (∼45.25%) dominated in fruits and leaves, respectively. High-performance liquid chromatography (HPLC) was employed to measure the alkaloid content of different plant parts. Significant correlations were observed between endophytic bacteria and alkaloids. Especially, Sphingomonas showed a significant positive correlation with sanguinarine and chelerythrine. All four alkaloids were negatively correlated with the microbiota of stems. The predicted result of PICRUST2 revealed that the synthesis of plant alkaloids might lead to a higher abundance of endophytic microorganisms with genes related to alkaloid synthesis, further demonstrated the correlation between bacterial communities and alkaloids. This study provided the first insight into the bacterial community composition in different parts of Macleaya cordata and the correlation between the endophytic bacteria and alkaloids.
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Affiliation(s)
- Fangying Lei
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Haonan Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shaodong Fu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Kai Zou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Li Zhou
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
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Finn DR, Bergk-Pinto B, Hazard C, Nicol GW, Tebbe CC, Vogel TM. Functional trait relationships demonstrate life strategies in terrestrial prokaryotes. FEMS Microbiol Ecol 2021; 97:6271318. [PMID: 33960387 DOI: 10.1093/femsec/fiab068] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/05/2021] [Indexed: 01/13/2023] Open
Abstract
Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.
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Affiliation(s)
- Damien R Finn
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Brisbane 4072, Australia.,Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France.,Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Bundesallee 65 Braunschweig 38116, Germany
| | - Benoît Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Christina Hazard
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Christoph C Tebbe
- Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Bundesallee 65 Braunschweig 38116, Germany
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
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Shen CZ, Zhang CJ, Chen J, Guo YP. Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae). Front Plant Sci 2021; 12:648026. [PMID: 34122473 PMCID: PMC8187803 DOI: 10.3389/fpls.2021.648026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/20/2021] [Indexed: 05/12/2023]
Abstract
Understanding the roles played by geography and ecology in driving species diversification and in the maintenance of species cohesion is the central objective of evolutionary and ecological studies. The multi-phased orogenesis of Qinghai-Tibetan Plateau (QTP) and global climate changes over late-Miocene has profoundly influenced the environments and evolution of organisms in this region and the vast areas of Asia. In this study, we investigate the lineage diversification of Chrysanthemum-group in subtribe Artemisiinae (tribe Anthemideae, Asteraceae) likely under the effects of climate changes during this period. Using DNA sequences of seven low-copy nuclear loci and nrITS and the coalescent analytical methods, a time-calibrated phylogeny of subtribe Artemisiinae was reconstructed with emphasis on Chrysanthemum-group. The monophyletic Chrysanthemum-group was well resolved into two major clades corresponding to Chrysanthemum and Ajania, two genera which can be well identified by capitulum morphology but have been intermingled in previous plastid and ITS trees. Within Chrysanthemum, a later divergence between Ch. indicum-complex and Ch. zawadskii-complex can be recognized. The time frames of these sequential divergences coincide with the late Cenozoic uplift of the Northern QTP and the concomitant climatic heterogeneity between eastern and inland Asia. Reconstruction of historical biogeography suggested the origin of Chrysanthemum-group in Central Asia, followed by eastward migration of Chrysanthemum and in situ diversification of Ajania. Within Chrysanthemum, Ch. indicum-complex and Ch. zawadskii-complex exhibited contemporary distributional division, the former in more southern and the latter in more northern regions. The geographic structure of the three lineages in Chrysanthemum-group have been associated with the niche differentiation, and environmental heterogenization in Asia interior.
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Affiliation(s)
- Chu-Ze Shen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chu-Jie Zhang
- School of Life Sciences, Peking University, Beijing, China
| | - Jie Chen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Yan-Ping Guo
- School of Life Sciences, Peking University, Beijing, China
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38
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Ndayambaje P, Wei L, Zhang T, Li Y, Liu L, Huang X, Liu C. Niche separation and weak interactions in the high tidal zone of saltmarsh-mangrove mixing communities. Ecol Evol 2021; 11:3871-3883. [PMID: 33976781 PMCID: PMC8093676 DOI: 10.1002/ece3.7263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/29/2020] [Accepted: 01/09/2021] [Indexed: 11/15/2022] Open
Abstract
Saltmarsh-mangrove ecotones occur at the boundary of the natural geographic distribution of mangroves and salt marshes. Climate warming and species invasion can also drive the formation of saltmarsh-mangrove mixing communities. How these coastal species live together in a "new" mixed community is important in predicting the dynamic of saltmarsh-mangrove ecosystems as affected by ongoing climate change or human activities. To date, the understanding of species interactions has been rare on adult species in these ecotones.Two typical coastal wetlands were selected as cases to understand how mangrove and saltmarsh species living together in the ecotones. The leaves of seven species were sampled from these coastal wetlands based on their distribution patterns (living alone or coexisting) in the high tidal zone, and seven commonly used functional traits of these species were analyzed.We found niche separation between saltmarsh and mangrove species, which is probably due to the different adaptive strategies they adopted to deal with intertidal environments.Weak interactions between coexisting species were dominated in the high tidal zone of the two saltmarsh-mangrove communities, which could be driven by both niche differentiation and neutral theory.Synthesis. Our field study implies a potential opportunity to establish a multispecies community in the high tidal zone of saltmarsh-mangrove ecotones, where the sediment was characterized by low salinity and high nitrogen.
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Affiliation(s)
- Patrick Ndayambaje
- Key Laboratory of Urban Pollutant ConversionInstitute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lili Wei
- Key Laboratory of Urban Pollutant ConversionInstitute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Tingfeng Zhang
- Key Laboratory of Urban Pollutant ConversionInstitute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Lin Liu
- Key Laboratory of Urban Pollutant ConversionInstitute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Xu Huang
- Key Laboratory of Urban Pollutant ConversionInstitute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Chaoxiang Liu
- Key Laboratory of Urban Pollutant ConversionInstitute of Urban EnvironmentChinese Academy of SciencesXiamenChina
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Cerasoli F, Besnard A, Marchand M, D'Alessandro P, Iannella M, Biondi M. Determinants of habitat suitability models transferability across geographically disjunct populations: Insights from Vipera ursinii urs inii. Ecol Evol 2021; 11:3991-4011. [PMID: 33976789 PMCID: PMC8093743 DOI: 10.1002/ece3.7294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/30/2020] [Accepted: 01/25/2021] [Indexed: 11/08/2022] Open
Abstract
Transferability of habitat suitability models (HSMs), essential to accurately predict outside calibration conditions, has been seldom investigated at intraspecific level. We targeted Vipera ursinii ursinii, a meadow viper from southeastern France and central Italy, to assess determinants of transferability among geographically disjunct populations. We fitted HSMs upon occurrences of the Italian and French populations separately, as well as on the combined occurrence dataset. Internal transferability of HSMs, on spatially independent test data drawn from the calibration region, and their external transferability on the geographically disjunct populations were evaluated according to (a) use of full or spatially rarefied presence datasets; (b) ecology-driven or statistics-driven filtering of predictors; (c) modeling algorithm, testing generalized additive models and gradient boosting models; and (d) multivariate environmental novelty within test data. Niche overlap between French and Italian populations was also tested. Niche overlap was low, but niche divergence between the two populations' clusters was not corroborated. Nonetheless, wider niche breadth and heterogeneity of background environmental conditions characterizing the French populations led to low intercluster transferability. Although models fitted on the combined datasets did not attain consistently higher internal transferability than those separately fitted for the French and Italian populations, ensemble projection from the HSMs fitted on the joint occurrences produced more consistent suitability predictions across the full range of V. u. ursinii. Spatial thinning of occurrences ameliorated internal transferability but did not affect external transferability. The two approaches to predictors filtering did not differ in transferability of the respective HSMs but led to discrepant estimated environment-occurrence relationships and spatial predictions, while the two algorithms attained different relative rankings depending on the considered prediction task. Multivariate novelty of projection sites was negatively correlated to both internal transferability and external transferability. Our findings clarify issues researchers should keep in mind when using HSMs to get predictions across geographically disjunct populations.
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Affiliation(s)
- Francesco Cerasoli
- Department of Life, Health and Environmental Sciences—Environmental Sciences Sect.University of L'AquilaL'AquilaItaly
| | - Aurélien Besnard
- CEFE UMR 5175CNRSPSL Research UniversityUniversité Paul‐Valéry Montpellier, EPHEMontpellierFrance
| | - Marc‐Antoine Marchand
- Conservatoire d'Espaces Naturels de Provence‐Alpes‐Côte d'AzurPôle Alpes du SudSisteronFrance
| | - Paola D'Alessandro
- Department of Life, Health and Environmental Sciences—Environmental Sciences Sect.University of L'AquilaL'AquilaItaly
| | - Mattia Iannella
- Department of Life, Health and Environmental Sciences—Environmental Sciences Sect.University of L'AquilaL'AquilaItaly
| | - Maurizio Biondi
- Department of Life, Health and Environmental Sciences—Environmental Sciences Sect.University of L'AquilaL'AquilaItaly
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40
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Wittorf L, Roger F, Alsterberg C, Gamfeldt L, Hulth S, Sundbäck K, Jones CM, Hallin S. Habitat diversity and type govern potential nitrogen loss by denitrification in coastal sediments and differences in ecosystem-level diversities of disparate N2O reducing communities. FEMS Microbiol Ecol 2021; 96:5871200. [PMID: 32662514 PMCID: PMC7428367 DOI: 10.1093/femsec/fiaa091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/12/2020] [Indexed: 01/28/2023] Open
Abstract
In coastal sediments, excess nitrogen is removed primarily by denitrification. However, losses in habitat diversity may reduce the functional diversity of microbial communities that drive this important filter function. We examined how habitat type and habitat diversity affects denitrification and the abundance and diversity of denitrifying and N2O reducing communities in illuminated shallow-water sediments. In a mesocosm experiment, cores from four habitats were incubated in different combinations, representing ecosystems with different habitat diversities. We hypothesized that habitat diversity promotes the diversity of N2O reducing communities and genetic potential for denitrification, thereby influencing denitrification rates. We also hypothesized that this will depend on the identity of the habitats. Habitat diversity positively affected ecosystem-level diversity of clade II N2O reducing communities, however neither clade I nosZ communities nor denitrification activity were affected. The composition of N2O reducing communities was determined by habitat type, and functional gene abundances indicated that silty mud and sandy sediments had higher genetic potentials for denitrification and N2O reduction than cyanobacterial mat and Ruppia maritima meadow sediments. These results indicate that loss of habitat diversity and specific habitats could have negative impacts on denitrification and N2O reduction, which underpin the capacity for nitrogen removal in coastal ecosystems.
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Affiliation(s)
- Lea Wittorf
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Fabian Roger
- University of Gothenburg, Department of Marine Sciences, Gothenburg, Sweden
| | | | - Lars Gamfeldt
- University of Gothenburg, Department of Marine Sciences, Gothenburg, Sweden
| | - Stefan Hulth
- University of Gothenburg, Department of Marine Sciences, Gothenburg, Sweden
| | - Kristina Sundbäck
- University of Gothenburg, Department of Marine Sciences, Gothenburg, Sweden
| | - Christopher M Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
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Wang X, Lu L, Zhou X, Tang X, Kuang L, Chen J, Shan J, Lu H, Qin H, Adams J, Wang B. Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary. Front Microbiol 2021; 11:618287. [PMID: 33584582 PMCID: PMC7873905 DOI: 10.3389/fmicb.2020.618287] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 01/13/2023] Open
Abstract
The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO3–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO3–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO3–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.
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Affiliation(s)
- Xinxin Wang
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China.,Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
| | - Xue Zhou
- College of Agricultural Engineering, Hohai University, Nanjing, China
| | - Xiufeng Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Kuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Junhui Chen
- Key State Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Hua Qin
- Key State Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jonathan Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Manktelow CJ, White H, Crickmore N, Raymond B. Divergence in environmental adaptation between terrestrial clades of the Bacillus cereus group. FEMS Microbiol Ecol 2020; 97:5974271. [PMID: 33175127 DOI: 10.1093/femsec/fiaa228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/06/2020] [Indexed: 12/25/2022] Open
Abstract
The Bacillus cereus group encompasses beneficial and harmful species in diverse niches and has a much debated taxonomy. Investigating whether selection has led to ecological divergence between phylogenetic clades can help understand the basis of speciation, and has implications for predicting biological safety across this group. Using three most terrestrial species in this group (B. cereus, Bacillus thuringiensis and Bacillus mycoides) we charactererized ecological specialization in terms of resource use, thermal adaptation and fitness in different environmental conditions and tested whether taxonomic species or phylogenetic clade best explained phenotypic variation. All isolates grew vigorously in protein rich media and insect cadavers, but exploitation of soil or plant derived nutrients was similarly weak for all. For B. thuringiensis and B. mycoides, clade and taxonomic species were important predictors of relative fitness in insect infections. Fully psychrotolerant isolates could outcompete B. thuringiensis in insects at low temperature, although psychrotolerance predicted growth in artificial media better than clade. In contrast to predictions, isolates in the Bacillus anthracis clade had sub-optimal growth at 37°C. The common ecological niche in these terrestrial B. cereus species is the ability to exploit protein rich resources such as cadavers. However, selection has led to different phylogenetic groups developing different strategies for accessing this resource. Thus, clades, as well as traditional taxonomic phenotypes, predict biologically important traits.
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Affiliation(s)
- C James Manktelow
- Centre for Ecology and Conservation, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
| | - Hugh White
- Centre for Ecology and Conservation, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Ben Raymond
- Centre for Ecology and Conservation, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
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Liang D, Ouyang Y, Tiemann L, Robertson GP. Niche Differentiation of Bacterial Versus Archaeal Soil Nitrifiers Induced by Ammonium Inhibition Along a Management Gradient. Front Microbiol 2020; 11:568588. [PMID: 33281763 PMCID: PMC7689314 DOI: 10.3389/fmicb.2020.568588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
Soil nitrification, mediated mainly by ammonia oxidizing archaea (AOA) and bacteria (AOB), converts ammonium (NH4+) to nitrite (NO2−) and thence nitrate (NO3−). To better understand ecological differences between AOA and AOB, we investigated the nitrification kinetics of AOA and AOB under eight replicated cropped and unmanaged ecosystems (including two fertilized natural systems) along a long-term management intensity gradient in the upper U.S. Midwest. For five of eight ecosystems, AOB but not AOA exhibited Haldane kinetics (inhibited by high NH4+ additions), especially in perennial and successional systems. In contrast, AOA predominantly exhibited Michaelis-Menten kinetics, suggesting greater resistance to high nitrogen inputs than AOB. These responses suggest the potential for NH4+-induced niche differentiation between AOA and AOB. Additionally, long-term fertilization significantly enhanced maximum nitrification rates (Vmax) in the early successional systems for both AOA and AOB, but not in the deciduous forest systems. This was likely due to pH suppression of nitrification in the acidic forest soils, corroborated by a positive correlation of Vmax with soil pH but not with amoA gene abundance. Results also demonstrated that soil nitrification potentials were relatively stable, as there were no seasonal differences. Overall, results suggest that (1) NH4+ inhibition of AOB but not AOA could be another factor contributing to niche differentiation between AOA and AOB in soil, and (2) nitrification by both AOA and AOB can be significantly promoted by long-term nitrogen inputs.
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Affiliation(s)
- Di Liang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States.,W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
| | - Yang Ouyang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - Lisa Tiemann
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - G Philip Robertson
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States.,W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
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Morgan EJ, Čertner M, Lučanová M, Kubíková K, Marhold K, Kolář F. Niche similarity in diploid-autotetraploid contact zones of Arabidopsis arenosa across spatial scales. Am J Bot 2020; 107:1375-1388. [PMID: 32974906 DOI: 10.1002/ajb2.1534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Whole genome duplication is a major evolutionary event, but its role in ecological divergence remains equivocal. When populations of different ploidy (cytotypes) overlap in space, "contact zones" are formed, allowing the study of evolutionary mechanisms contributing toward ploidy divergence. Multiple contact zones per species' range are often described but rarely leveraged as natural replicates. We explored whether the strength of niche differentiation of diploid and autotetraploid Arabidopsis arenosa varies over distinct contact zones and if the frequency of triploids decreases from seedling to adult stage. METHODS We characterized ploidy composition and habitat preferences in 264 populations across three contact zones using climatic niche modeling. Ecological differences of cytotypes were also assessed using local vegetation surveys at 110 populations within two contact zones, and at the finer scale within five mixed-ploidy sites. This was complemented by flow cytometry of seedlings. RESULTS We found no niche differences between diploid and tetraploid populations within contact zones for either climatic or local environmental variables. Comparisons of cytotypes within mixed-ploidy sites found weak niche differences that were inconsistent in direction. Triploid individuals were virtually absent (0.14%) in the field, and they were at a similarly low frequency (0.2%) in ex situ germinated seedlings. CONCLUSIONS This study demonstrates the strength in investigating different spatial scales across several contact zones when addressing ecological niche differentiation between ploidies. The lack of consistent habitat differentiation of ploidies across the scales and locations supports the recently emerging picture that processes other than ecological differentiation may underlie ploidy coexistence in diploid-autopolyploid systems.
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Affiliation(s)
- Emma J Morgan
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Magdalena Lučanová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, CZ-370 05, České Budějovice, Czech Republic
| | - Kateřina Kubíková
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
| | - Karol Marhold
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23, Bratislava, Slovak Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, AT-6020, Innsbruck, Austria
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Ohdo T, Takahashi K. Plant species richness and community assembly along gradients of elevation and soil nitrogen availability. AoB Plants 2020; 12:plaa014. [PMID: 32467749 PMCID: PMC7243275 DOI: 10.1093/aobpla/plaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 04/11/2020] [Indexed: 06/11/2023]
Abstract
Environmental filters affect community assembly through the functional traits of species. However, the process of community assembly remains unclear because of the complex interactions among the many biotic and abiotic factors. This study aimed to examine the community assembly process of vascular plants along gradients of elevation (45‒2500 m a.s.l.) and soil nitrogen availability. This study examined the trait distribution patterns of four functional traits (plant height, leaf area, specific leaf area and leaf nitrogen concentration) of vascular plants (trees, herbs and ferns) in central Japan, using null model testing. The number of species decreased and increased at high elevations for tree species and herb and fern species, respectively. The numbers of both tree species and herb and fern species were positively correlated with soil nitrogen availability. Community-weighted means (CWMs) of the four traits decreased with elevation. CWMs and ranges of the three leaf traits were positively correlated with soil nitrogen availability. The community-weighted variance of plant height was higher at higher elevations, indicating that niche differentiation of vertical stratum in habitats with a low canopy was important for community assembly. This study suggests that severe climatic conditions reduce the number of tree species and the canopy height at high elevations, leading to increases in the number of herb and fern species due to increased light intensity at the forest floor. The elevational change of leaf traits also indicates the change of adaptive leaf traits. It further suggests that lower nitrogen availability decreases the number of tree, herb and fern species by excluding those species with leaf traits unsuited to lower nitrogen availability. Therefore, community structure is most likely regulated by both elevation and soil nitrogen availability.
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Affiliation(s)
- Taro Ohdo
- Graduate School of Science and Technology, Shinshu University, Asahi, Matsumoto, Japan
| | - Koichi Takahashi
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, Japan
- Institute of Mountain Science, Shinshu University, Asahi, Matsumoto, Japan
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Zhang S, Li B, Yu Z, Meng F. Aggregate size-dependence of bacterial community separation in a full-scale membrane bioreactor plant. FEMS Microbiol Ecol 2020; 96:5818762. [PMID: 32275301 DOI: 10.1093/femsec/fiaa060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/02/2020] [Indexed: 11/13/2022] Open
Abstract
The size of bacterial aggregates can determine both nutrient removal and sludge/water separation in activated sludge processes. In this study, the bacterial community structures and network associations of different sized aggregates obtained from a full-scale membrane bioreactor plant over a one-year period were investigated. Our results showed that biodiversity of larger sized aggregates was significantly higher than that of smaller ones and that the bacterial compositions of different sized aggregates differed significantly from each other. Bacteria related to nutrient removal (e.g. denitrification, hydrolysis and fermentation) were found to be significantly more abundant in larger aggregates than smaller ones. Network analysis revealed significant difference in species-species interactions, topological roles of individual OTU and keystone populations among different sized aggregates. Moreover, the occurrence of keystone OTUs affiliated with denitrifiers (Thermomonas) in networks of large and medium aggregates may suggest that denitrification influences bacterial interactions in large and medium aggregates. Overall, our results indicate the aggregates size-dependence of bacterial community separation in activated sludge. The current findings not only can provide guidance for process design and operation optimization, but also highlight the necessity for paying more attentions to the aggregate-based community, metabolic function and gene expression of activated sludge in future studies.
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Affiliation(s)
- Shaoqing Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
| | - Bing Li
- Division of Energy and Environment, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Zhong Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
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Samad MS, Lee HJ, Cerbin S, Meima-Franke M, Bodelier PLE. Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes. Front Microbiol 2020; 11:582. [PMID: 32390961 PMCID: PMC7190982 DOI: 10.3389/fmicb.2020.00582] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their "host". However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PA, and zooplankton associated microbes and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analyzed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PA. Surprisingly, genera of methane-oxidizing bacteria, methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PA. Our study clearly demonstrates niche differentiation of pelagic microbes and their potential link to biogeochemical cycling in freshwater systems.
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Affiliation(s)
- Md Sainur Samad
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, Gunsan, South Korea
| | - Slawek Cerbin
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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48
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Luimstra VM, Verspagen JMH, Xu T, Schuurmans JM, Huisman J. Changes in water color shift competition between phytoplankton species with contrasting light-harvesting strategies. Ecology 2020; 101:e02951. [PMID: 31840230 PMCID: PMC7079016 DOI: 10.1002/ecy.2951] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/13/2019] [Accepted: 11/11/2019] [Indexed: 12/28/2022]
Abstract
The color of many lakes and seas is changing, which is likely to affect the species composition of freshwater and marine phytoplankton communities. For example, cyanobacteria with phycobilisomes as light-harvesting antennae can effectively utilize green or orange-red light. However, recent studies show that they use blue light much less efficiently than phytoplankton species with chlorophyll-based light-harvesting complexes, even though both phytoplankton groups may absorb blue light to a similar extent. Can we advance ecological theory to predict how these differences in light-harvesting strategy affect competition between phytoplankton species? Here, we develop a new resource competition model in which the absorption and utilization efficiency of different colors of light are varied independently. The model was parameterized using monoculture experiments with a freshwater cyanobacterium and green alga, as representatives of phytoplankton with phycobilisome-based vs. chlorophyll-based light-harvesting antennae. The parameterized model was subsequently tested in a series of competition experiments. In agreement with the model predictions, the green alga won the competition in blue light whereas the cyanobacterium won in red light, irrespective of the initial relative abundances of the species. These results are in line with observed changes in phytoplankton community structure in response to lake brownification. Similarly, in marine waters, the model predicts dominance of Prochlorococcus with chlorophyll-based light-harvesting complexes in blue light but dominance of Synechococcus with phycobilisomes in green light, with a broad range of coexistence in between. These predictions agree well with the known biogeographical distributions of these two highly abundant marine taxa. Our results offer a novel trait-based approach to understand and predict competition between phytoplankton species with different photosynthetic pigments and light-harvesting strategies.
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Affiliation(s)
- Veerle M. Luimstra
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamPO Box 94240Amsterdam1090 GEThe Netherlands
- WetsusEuropean Centre of Excellence for Sustainable Water TechnologyOostergoweg 9Leeuwarden8911 MAThe Netherlands
| | - Jolanda M. H. Verspagen
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamPO Box 94240Amsterdam1090 GEThe Netherlands
| | - Tianshuo Xu
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamPO Box 94240Amsterdam1090 GEThe Netherlands
| | - J. Merijn Schuurmans
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamPO Box 94240Amsterdam1090 GEThe Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamPO Box 94240Amsterdam1090 GEThe Netherlands
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Dumbrell AJ. Size matters in regulating the biodiversity of tropical forest soils. Mol Ecol 2020; 28:525-527. [PMID: 30793869 DOI: 10.1111/mec.14996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022]
Abstract
Tropical forests have long fascinated ecologists, inspiring a plethora of research into the mechanisms regulating their immense biodiversity, which originally captured the interests of early natural historians and explorers, and that still persists to this day. A new focus of this research emerged in the early 2000s highlighting the potential role of neutral (stochastic) processes in regulating the composition and diversity of tropical forest communities, and thus the maintenance of a large portion of global biodiversity (Hubbell, ). This strictly contrasted the long-held belief that communities assembled via the sorting of species (and their abundances) via a deterministic response to local abiotic and biotic environmental conditions, reflecting the niche of each species (Leibold & McPeek, ). Yet, it is unlikely that the assembly of any community is solely governed by either stochastic or deterministic processes, but instead a combination of both. However, whether deterministic processes via niche-based environmental sorting of species, or stochastic processes reflecting pattens of dispersal limitation, neutral effects and ecological drift dominate is often unclear. This prompts questions as to whether the relative influence of one process over another is dependent on the scale (spatial or temporal) or context of the study, or specific traits of the taxa under investigation (e.g., body size). In a From the Cover paper in this issue of Molecular Ecology, Zinger et al. () tackle all these issues and show, among other things, that for soil microbes and mesofauna from tropical forests, the relative contribution of stochastic and deterministic processes in assembling their communities is strongly dependent on the body size or the studied taxa.
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Affiliation(s)
- Alex J Dumbrell
- School of Biological Sciences, University of Essex, Colchester, Essex, UK
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50
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Janeček Š, Chmel K, Uceda Gómez G, Janečková P, Chmelová E, Sejfová Z, Luma Ewome F. Ecological fitting is a sufficient driver of tight interactions between sunbirds and ornithophilous plants. Ecol Evol 2020; 10:1784-1793. [PMID: 32128116 PMCID: PMC7042734 DOI: 10.1002/ece3.5942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/22/2019] [Accepted: 11/28/2019] [Indexed: 11/11/2022] Open
Abstract
Plant-bird pollination interactions evolved independently on different continents. Specific adaptations can lead to their restriction when potential partners from distant evolutionary trajectories come into contact. Alternatively, these interactions can be enabled by convergent evolution and subsequent ecological fitting.We studied the interactions between New World plants from the genus Heliconia, Asian plants of genus Etlingera and African sunbirds on a local farm in Cameroon. Heliconia spp. evolved together with hummingbirds and Etlingera spp. with spiderhunters -an oriental subgroup of the sunbird family.Sunbirds fed on all studied plants and individual plant species were visited by a different sunbird spectrum. We experimentally documented a higher number of germinated pollen grains in sunbird-visited flowers of Etlingera spp. For Heliconia spp., this experiment was not successful and pollen tubes were rarely observed, even in hand-pollinated flowers, where enough pollen was deposited. The analyses of contacts with plant reproductive organs nevertheless confirmed that sunbirds are good pollen vectors for both Heliconia and Etlingera species.Our study demonstrated a high ecological fit between actors of distinct evolutionary history and the general validity of bird-pollination syndrome. We moreover show that trait matching and niche differentiation are important ecological processes also in semi-artificial plant-pollinator systems.
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Affiliation(s)
- Štěpán Janeček
- Department of EcologyFaculty of ScienceCharles University in PraguePrahaCzech Republic
| | - Kryštof Chmel
- Department of EcologyFaculty of ScienceCharles University in PraguePrahaCzech Republic
- Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic
| | - Guillermo Uceda Gómez
- Department of EcologyFaculty of ScienceCharles University in PraguePrahaCzech Republic
| | - Petra Janečková
- Department of EcologyFaculty of ScienceCharles University in PraguePrahaCzech Republic
- University of South BohemiaČeské BudějoviceCzech Republic
| | - Eliška Chmelová
- Department of EcologyFaculty of ScienceCharles University in PraguePrahaCzech Republic
- Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic
| | - Zuzana Sejfová
- Department of EcologyFaculty of ScienceCharles University in PraguePrahaCzech Republic
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