1
|
Çakmak T. Comparative analysis of soil nematode biodiversity from five different fruit orchards in Osmaneli district, Bilecik, Türkiye. J Nematol 2024; 56:20240001. [PMID: 38495932 PMCID: PMC10940273 DOI: 10.2478/jofnem-2024-0001] [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: 01/06/2024] [Indexed: 03/19/2024] Open
Abstract
Nematode population densities were determined in 60 soil and root samples collected from 6 fruit orchards in the Bilecik province (western Turkey), between April 2022 and June 2022. The total number of identified nematodes have reached up to 2418 individuals (number of female: 1036; male: 154; and juvenile: 1228). They belong to 54 species, 54 genera, 33 families and 11 orders. Plant parasitic nematodes that were detected mostly are listed as follows: Helicotylenchus (6,12 %), Pratylenchus (5,74 %), Paratylenchus (4.83 %), Xiphinema (3,06 %), Tylenchorhynchus (2,19 %), Malenchus (1.94 %) and Tylenchus (1.19 %). According to the maturity index analysis, mean values showed the highest maturity level at peach trees (MI value: 3,52), followed by; walnut trees (MI value: 2.49), cherry trees (MI value: 2.15), nectarine trees (MI value: 1.86), plum trees (MI value: 1.57), and olive trees (MI value: 1.42). Mostly the diverse group in terms of species richness was within the order Dorylaimida. The nematodes associated with peach and walnut trees here showed the most stable environments in terms of soil nematode community structure.
Collapse
Affiliation(s)
- Taylan Çakmak
- Department of Agricultural Biotechnology, Düzce University Faculty of Agriculture
| |
Collapse
|
2
|
Zipkin EF, Doser JW, Davis CL, Leuenberger W, Ayebare S, Davis KL. Integrated community models: A framework combining multispecies data sources to estimate the status, trends and dynamics of biodiversity. J Anim Ecol 2023; 92:2248-2262. [PMID: 37880838 DOI: 10.1111/1365-2656.14012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/28/2023] [Accepted: 09/07/2023] [Indexed: 10/27/2023]
Abstract
Data deficiencies among rare or cryptic species preclude assessment of community-level processes using many existing approaches, limiting our understanding of the trends and stressors for large numbers of species. Yet evaluating the dynamics of whole communities, not just common or charismatic species, is critical to understanding and the responses of biodiversity to ongoing environmental pressures. A recent surge in both public science and government-funded data collection efforts has led to a wealth of biodiversity data. However, these data collection programmes use a wide range of sampling protocols (from unstructured, opportunistic observations of wildlife to well-structured, design-based programmes) and record information at a variety of spatiotemporal scales. As a result, available biodiversity data vary substantially in quantity and information content, which must be carefully reconciled for meaningful ecological analysis. Hierarchical modelling, including single-species integrated models and hierarchical community models, has improved our ability to assess and predict biodiversity trends and processes. Here, we highlight the emerging 'integrated community modelling' framework that combines both data integration and community modelling to improve inferences on species- and community-level dynamics. We illustrate the framework with a series of worked examples. Our three case studies demonstrate how integrated community models can be used to extend the geographic scope when evaluating species distributions and community-level richness patterns; discern population and community trends over time; and estimate demographic rates and population growth for communities of sympatric species. We implemented these worked examples using multiple software methods through the R platform via packages with formula-based interfaces and through development of custom code in JAGS, NIMBLE and Stan. Integrated community models provide an exciting approach to model biological and observational processes for multiple species using multiple data types and sources simultaneously, thus accounting for uncertainty and sampling error within a unified framework. By leveraging the combined benefits of both data integration and community modelling, integrated community models can produce valuable information about both common and rare species as well as community-level dynamics, allowing for holistic evaluation of the effects of global change on biodiversity.
Collapse
Affiliation(s)
- Elise F Zipkin
- Department of Integrative Biology; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Jeffrey W Doser
- Department of Integrative Biology; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Courtney L Davis
- Department of Integrative Biology; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Wendy Leuenberger
- Department of Integrative Biology; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Samuel Ayebare
- Department of Integrative Biology; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Kayla L Davis
- Department of Integrative Biology; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
3
|
Govender A, Singh S, Groeneveld J, Pillay S, Willows-Munro S. Metabarcoding analysis of marine zooplankton confirms the ecological role of a sheltered bight along an exposed continental shelf. Mol Ecol 2023; 32:6210-6222. [PMID: 35712991 DOI: 10.1111/mec.16567] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/08/2021] [Revised: 05/17/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
Zooplankton plays an essential role in marine ecosystems as the link between primary producers (phytoplankton) and higher trophic levels in food webs, and as a dynamic pool of recruits for invertebrates and fish. Zooplankton communities are diverse with a patchy distribution at different spatial scales, influenced by oceanographic processes. The continental shelf of eastern South Africa is narrow and exposed to the western-boundary Agulhas Current, with some shelter against strong directional flow provided by the broader KwaZulu-Natal Bight, a coastal offset adjacent to an estuary. We compared zooplankton species richness, diversity and relative abundance of key taxa among sheltered and exposed shelf areas using metabarcoding and community analysis, to explore the ecological role of the bight in a highly dynamic ocean region. Metabarcoding recovered higher richness and diversity at a finer resolution than could previously be achieved with traditional microscopy. Of 271 operational taxonomic units (OTUs) recovered through metabarcoding, 63% could be matched with >95% sequence similarity to reference barcodes. OTUs were dominated by malacostracan crustaceans (161 spp.), ray-finned fishes (45 spp.) and copepods (28 spp.). Species richness, diversity and the relative abundance of key taxa differed between sheltered and exposed shelf areas. Lower species richness in the bight was partly attributed to structurally homogeneous benthic habitats, and an associated reduction of meroplanktonic species originating from local benthic-pelagic exchange. High relative abundance of a ray-finned fish in the bight, as observed based on fish eggs and read counts, confirmed that the bight is an important fish spawning area. Overall, zooplankton metabarcoding outputs were congruent with findings of previous ecological research using more traditional methods of observation.
Collapse
Affiliation(s)
- Ashrenee Govender
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Oceanographic Research Institute, Durban, South Africa
| | - Sohana Singh
- Oceanographic Research Institute, Durban, South Africa
| | - Johan Groeneveld
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Oceanographic Research Institute, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| |
Collapse
|
4
|
Klaes S, Madan S, Deobald D, Cooper M, Adrian L. GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry. Int J Mol Sci 2023; 24:15692. [PMID: 37958676 PMCID: PMC10649880 DOI: 10.3390/ijms242115692] [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: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Profiling bacterial populations in mixed communities is a common task in microbiology. Sequencing of 16S small subunit ribosomal-RNA (16S rRNA) gene amplicons is a widely accepted and functional approach but relies on amplification primers and cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping is an effective alternative for taxonomically profiling microorganisms. We suggest that targeted proteotyping approaches can complement traditional population analyses. Therefore, we describe an approach to assess bacterial community compositions at the family level using the taxonomic marker protein GroEL, which is ubiquitously found in bacteria, except a few obligate intracellular species. We refer to our method as GroEL-proteotyping. GroEL-proteotyping is based on high-resolution tandem mass spectrometry of GroEL peptides and identification of GroEL-derived taxa via a Galaxy workflow and a subsequent Python-based analysis script. Its advantage is that it can be performed with a curated and extendable sample-independent database and that GroEL can be pre-separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to reduce sample complexity, improving GroEL identification while simultaneously decreasing the instrument time. GroEL-proteotyping was validated by employing it on a comprehensive raw dataset obtained through a metaproteome approach from synthetic microbial communities as well as real human gut samples. Our data show that GroEL-proteotyping enables fast and straightforward profiling of highly abundant taxa in bacterial communities at reasonable taxonomic resolution.
Collapse
Affiliation(s)
- Simon Klaes
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Shobhit Madan
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty of Engineering, Ansbach University of Applied Sciences, 91522 Ansbach, Germany
| | - Darja Deobald
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
| | - Myriel Cooper
- Faculty III Process Sciences, Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, 10587 Berlin, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| |
Collapse
|
5
|
Chen B, Dong K, Xu Y, Jiang M, Zheng J, Zeng H, Zhang X, Chen Y, Li H. Biodegradation of nitrate and p-bromophenol using hydrogen-based membrane biofilm reactors in parallel. Environ Technol 2023:1-15. [PMID: 37729639 DOI: 10.1080/09593330.2023.2259091] [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] [Received: 03/03/2023] [Accepted: 04/28/2023] [Indexed: 09/22/2023]
Abstract
ABSTRACTP-bromophenol (4-BP) is a toxic halogenated phenolic organic compound. The conventional treatment processes for 4-BP elimination are costly and inefficient, with complete mineralization remaining a challenge for water treatment. To overcome these limitations, we investigated the treatment of 4-BP in a membrane biofilm reactor (MBfR) using hydrogen as an electron donor. The pathway of 4-BP degradation within the H2-MBfR was investigated through long-term operational experiments by considering the effect of nitrate and 4-BP concentrations, hydrogen partial pressure, static experiments, and microbial community diversity, which was studied using 16S rRNA. The results showed that H2-MBfR could quickly remove approximately 100% of 4-BP (up to 20 mg/L), with minimal intermediate product accumulation and 10 mg/L of nitrate continuously reduced. The microbial community structure showed that the presence of H2 created an anaerobic environment, and Thauera was the dominant functional genus involved in the degradation of 4-BP. The genes encoding related enzymes were further enhanced. This study provides an economically viable and environmentally friendly bioremediation technique for water bodies that contain 4-BP and nitrates.
Collapse
Affiliation(s)
- Bo Chen
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Kun Dong
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Yufeng Xu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin, People's Republic of China
| | - Minmin Jiang
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, People's Republic of China
| | - Junjian Zheng
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, People's Republic of China
| | - Honghu Zeng
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Xuehong Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Yuchao Chen
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Haixiang Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin, People's Republic of China
| |
Collapse
|
6
|
Chakraborty M, Acharya D, Dutta TK. Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches. J Appl Microbiol 2023; 134:lxad208. [PMID: 37699793 DOI: 10.1093/jambio/lxad208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/17/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
AIMS The bacterial communities associated with the gastrointestinal (GI) tract are primarily involved in digestion, physiology, and the immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota. METHODS AND RESULTS Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising 16 Gram-negative, and 7 Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important GI bacteria, primarily dominated by Proteobacteria, Firmicutes, and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively. CONCLUSIONS A combination of these approaches provided the differential GI-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential. IMPACT STATEMENT The study explored the diversity of gut microbiota in hilsa, one of the most preferred nutritious dietary fish, captured from freshwater and seawater habitats, which may encourage to comprehend the composition of the gut microbiome in relation to the migratory behavior and polyunsaturated fatty acid profile of anadromous fish in general.
Collapse
Affiliation(s)
- Megha Chakraborty
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
| | - Debarun Acharya
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
| |
Collapse
|
7
|
Gräf T, Koch V, Köser J, Fischer J, Tessarek C, Filser J. Biotic and Abiotic Interactions in Freshwater Mesocosms Determine Fate and Toxicity of CuO Nanoparticles. Environ Sci Technol 2023; 57:12376-12387. [PMID: 37561908 DOI: 10.1021/acs.est.3c00493] [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] [Indexed: 08/12/2023]
Abstract
Transformation, dissolution, and sorption of copper oxide nanoparticles (CuO-NP) play an important role in freshwater ecosystems. We present the first mesocosm experiment on the fate of CuO-NP and the dynamics of the zooplankton community over a period of 12 months. Increasingly low (0.08-0.28 mg Cu L-1) and high (0.99-2.99 mg Cu L-1) concentrations of CuO-NP and CuSO4 (0.10-0.34 mg Cu L-1) were tested in a multiple dosing scenario. At the high applied concentration (CuO-NP_H) CuO-NP aggregated and sank onto the sediment layer, where we recovered 63% of Cu applied. For the low concentration (CuO-NP_L) only 41% of applied copper could be recovered in the sediment. In the water column, the percentage of initially applied Cu recovered was on average 3-fold higher for CuO-NP_L than for CuO-NP_H. Zooplankton abundance was substantially compromised in the treatments CuSO4 (p < 0.001) and CuO-NP_L (p < 0.001). Community analysis indicated that Cladocera were most affected (bk = -0.49), followed by Nematocera (bk = -0.32). The abundance of Cladocera over time and of Dixidae in summer was significantly reduced in the treatment CuO-NP_L (p < 0.001; p < 0.05) compared to the Control. Our results indicate a higher potential for negative impacts on the freshwater community when lower concentrations of CuO-NP (<0.1 mg Cu L-1) enter the ecosystem.
Collapse
Affiliation(s)
- Tonya Gräf
- FB 02 UFT - Centre for Environmental Research and Sustainable Technology, General and Theoretical Ecology, University of Bremen, Leobener Str. 6, 28359 Bremen, Germany
| | - Viviane Koch
- FB 02 UFT - Centre for Environmental Research and Sustainable Technology, General and Theoretical Ecology, University of Bremen, Leobener Str. 6, 28359 Bremen, Germany
| | - Jan Köser
- FB 02 UFT - Centre for Environmental Research and Sustainable Technology, Chemical Process Engineering, University of Bremen, Leobener Str. 6, 28359 Bremen, Germany
| | - Jonas Fischer
- FB 02 UFT - Centre for Environmental Research and Sustainable Technology, General and Theoretical Ecology, University of Bremen, Leobener Str. 6, 28359 Bremen, Germany
| | - Christian Tessarek
- Institute of Solid State Physics, University of Bremen, Otto-Hahn-Allee 1, 6, 28359 Bremen, Germany
| | - Juliane Filser
- FB 02 UFT - Centre for Environmental Research and Sustainable Technology, General and Theoretical Ecology, University of Bremen, Leobener Str. 6, 28359 Bremen, Germany
| |
Collapse
|
8
|
Gunathilaka MDKL, Bao S, Liu X, Li Y, Pan Y. Antibiotic Pollution of Planktonic Ecosystems: A Review Focused on Community Analysis and the Causal Chain Linking Individual- and Community-Level Responses. Environ Sci Technol 2023; 57:1199-1213. [PMID: 36628989 DOI: 10.1021/acs.est.2c06787] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Antibiotic pollution has become one of the most challenging environmental issues in aquatic ecosystems, with adverse effects on planktonic organisms that occupy the base of the aquatic food chain. However, research regarding this topic has not been systematically reviewed, especially in terms of community-level responses. In this review, we provide an overview of current antibiotic pollution in aquatic environments worldwide. Then, we summarize recent studies concerning the responses of planktonic communities to antibiotics, ranging from individual- to community-level responses. Studies have shown that extremely high concentrations of antibiotics can directly harm the growth and survival of plankton; however, such concentrations are rarely found in natural freshwater. It is more likely that environmentally relevant concentrations of antibiotics will affect the physiological, morphological, and behavioral characteristics of planktonic organisms; influence interspecific interactions among plankton species via asymmetrical responses in species traits; and thus alter the structure and function of the entire planktonic ecosystem. This review highlights the importance of community analysis in revealing antibiotic toxicity. We also encourage the establishment of the causal relationships between impacts at multiple scales in the future for predicting the community-level consequences of antibiotics based on the currently available individual-level evidence.
Collapse
Affiliation(s)
- M D K Lakmali Gunathilaka
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650091, China
- Yunnan International Cooperative Center of Plateau Lake Ecological Restoration and Watershed Management and Yunnan Think Tank of Ecological Civilization, Kunming, Yunnan 650091, China
- Department of Geography, University of Colombo, Colombo 00300, Sri Lanka
| | - Siyi Bao
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650091, China
- Yunnan International Cooperative Center of Plateau Lake Ecological Restoration and Watershed Management and Yunnan Think Tank of Ecological Civilization, Kunming, Yunnan 650091, China
| | - Xiaoxuan Liu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650091, China
- Yunnan International Cooperative Center of Plateau Lake Ecological Restoration and Watershed Management and Yunnan Think Tank of Ecological Civilization, Kunming, Yunnan 650091, China
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming 650091, People's Republic of China
| | - Ya Li
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650091, China
- Yunnan International Cooperative Center of Plateau Lake Ecological Restoration and Watershed Management and Yunnan Think Tank of Ecological Civilization, Kunming, Yunnan 650091, China
| | - Ying Pan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650091, China
- Yunnan International Cooperative Center of Plateau Lake Ecological Restoration and Watershed Management and Yunnan Think Tank of Ecological Civilization, Kunming, Yunnan 650091, China
| |
Collapse
|
9
|
Abstract
The role of the microbial community in mediating fish and plant co-culture is often considered the black box of aquaponics. Despite widespread recognition regarding the dependency of plants on their rhizosphere, the extent to which upstream aquaculture influences downstream hydroponic root communities has been poorly described in the literature. In this study we performed a taxonomic survey (16S rRNA metabarcoding) of microbial communities originating in the facility water source, hydroponic nutrient solution (HNS) sump, nutrient supplemented biofilter effluent (BF) sump, and recirculating aquaculture system tanks stocked with Nile tilapia (Oreochromis niloticus). Lettuce (Lactuca sativa) was then grown using the HNS and BF effluent under sterilized or mature (prior aquaponics/hydroponics lettuce culture water) conditions, likewise, the influence of probiotic addition or inoculation with soil-grown lettuce rhizosphere was assessed. Compositional similarities across treatments suggest that under soil-less conditions, plants are able to exert a stronger discriminatory influence on their rhizosphere composition than is done by colonization from upstream sources. Furthermore, cluster dendrograms grouped the sterilized and unsterilized treatments more consistently together than hydroponics and aquaponics treatments. These findings contradict conventional beliefs that microbial communities in the water column colonize roots based on their presence alone, ignoring the role that plants play in rhizosphere community selection.
Collapse
Affiliation(s)
- Victor Lobanov
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Karel J. Keesman
- Mathematical and Statistical Methods Group – Biometris, Wageningen University & Research, Wageningen, Netherlands
| | - Alyssa Joyce
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
10
|
BURLAKOVA LYUBOVE, KARATAYEV ALEXANDERY, HRYCIK ALLISONR, DANIEL SUSANE, MEHLER KNUT, RUDSTAM LARSG, WATKINS JAMESM, DERMOTT RONALD, SCHAROLD JILL, ELGIN ASHLEYK, NALEPA THOMAS. Six decades of Lake Ontario ecological history according to benthos. J Great Lakes Res 2022; 48:274-288. [PMID: 36092777 PMCID: PMC9454375 DOI: 10.1016/j.jglr.2021.03.006] [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] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The Laurentian Great Lakes have experienced multiple anthropogenic changes in the past century, including cultural eutrophication, phosphorus abatement initiatives, and the introduction of invasive species. Lake Ontario, the most downstream lake in the system, is considered to be among the most impaired. The benthos of Lake Ontario has been studied intensively in the last six decades and can provide insights into the impact of environmental changes over time. We used multivariate community analyses to examine temporal changes in community composition over the last 54 years, and to assess the major drivers of long-term changes in benthos. The benthic community of Lake Ontario underwent significant transformations that correspond with three major periods. The first period, termed the pre/early Dreissena period (1964-1990), was characterized by high densities of Diporeia, Sphaeriidae, and Tubificidae. During the next period defined by zebra mussel dominance (the 1990s) the same groups were still prevalent, but at altered densities. In the most recent period (2000s to present), which is characterized by the dominance and proliferation of quagga mussels deeper into the lake, the community has changed dramatically: Diporeia almost completely disappeared, Sphaeriidae have greatly declined, and densities of quagga mussels, Oligochaeta and Chironomidae have increased. The introduction of invasive dreissenids has changed the Lake Ontario benthic community, historically dominated by Diporeia, Oligochaeta and Sphaeriidae, to a community dominated by quagga mussels and Oligochaeta. Dreissenids, especially the quagga mussel, were the major drivers of these changes over the last half century.
Collapse
Affiliation(s)
- LYUBOV E. BURLAKOVA
- Great Lakes Center, SUNY Buffalo State, Buffalo, NY, USA
- Corresponding author: Phone: 716-878-5423, 716-878-4504, 716-878-4614, Fax: 716-878-6644,
| | | | | | | | - KNUT MEHLER
- Great Lakes Center, SUNY Buffalo State, Buffalo, NY, USA
| | - LARS G. RUDSTAM
- Cornell University, Department of Natural Resources, Ithaca, NY, 14850, USA
| | - JAMES M. WATKINS
- Cornell University, Department of Natural Resources, Ithaca, NY, 14850, USA
| | - RONALD DERMOTT
- Alumnus, Fisheries and Oceans Canada, Great Lakes Lab. Fisheries Aquatic Science, Burlington, ON, L7R4A6, Canada
| | - JILL SCHAROLD
- U.S. EPA Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA
| | - ASHLEY K. ELGIN
- NOAA Great Lakes Environmental Research Laboratory, Lake Michigan Field Station, 1431 Beach St., Muskegon, MI 49441, USA
| | - THOMAS NALEPA
- Water Center, University of Michigan, 214 S. State St., Ann Arbor, MI 48109, USA
| |
Collapse
|
11
|
Yu D, Zhao Y, Yin C, Liang F, Chen W. A Network Analysis of the Association Between Intergroup Contact and Intergroup Relations. Psychol Res Behav Manag 2022; 15:51-69. [PMID: 35027853 PMCID: PMC8752073 DOI: 10.2147/prbm.s336740] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022] Open
Abstract
PURPOSE Intergroup contact is an effective strategy to improve intergroup relationships. Although intergroup relationships have been studied extensively, the individual roles of quantity and quality of contact in relationships with cognition, emotion, and intention of behavior toward other ethnic minority groups are not fully understood. This study explores the situation via network analysis among Zhuang and Yao ethnic minorities in Southwest China. METHODS We investigated the quantity and quality of intergroup contact and cognition, emotion, and intention of behavior among a sample of 543 Zhuang and 490 Yao ethnic group members. Data were analyzed using the R-package. Network structures were analyzed via the Qgraph package, and the accuracy and stability of the network were measured via the Bootnet package; communities were detected via the Igraph package; bridge analyses were conducted via the Networktools package; and the network difference was compared via the Network Comparison Test package. RESULTS The results indicated perceived intimacy is the central node. Quantity of contact constructed a community with "perceived connection," "sense of community," "knowledge about out-group," and "perceived similarity." Meanwhile, quality of contact constructed a community with "intergroup attitude" and a "feeling thermometer." The remainder of the nodes constructed two additional communities. The network global connectivity and structure between the two ethnic groups were highly similar. CONCLUSION The study examined the quantity and quality of intergroup contact via network analysis for two ethnic minority groups. It was shown that the two groups' global network structures of intergroup contact and their effects are highly similar. Specifically, quantity and quality of contact produce different effects on intergroup relations. Quantity of contact has proximal effects, including instant cognitive and emotional response without depth cognition, while quality of contact has proximal effects that may change deep-seated cognition and subsequently improve intergroup relations.
Collapse
Affiliation(s)
- Dongfang Yu
- Center for Studies of Education and Psychology of Ethnic Minorities in Southwest China, Southwest University, Chongqing, People’s Republic of China
- Reader Service Dept, Guangxi University of Finance and Economics, Nanning, People’s Republic of China
| | - Yufang Zhao
- Center for Studies of Education and Psychology of Ethnic Minorities in Southwest China, Southwest University, Chongqing, People’s Republic of China
- Faculty of Psychology, Southwest University, Chongqing, People’s Republic of China
| | - Chenzu Yin
- School of Teacher Education, Hechi University, Hechi, People’s Republic of China
| | - Fangmei Liang
- School of Teacher Education, Hechi University, Hechi, People’s Republic of China
| | - Wenyu Chen
- College of Computer and Information Science, Southwest University, Chongqing, People’s Republic of China
| |
Collapse
|
12
|
Sikandar A, Khanum TA, Wang Y. Biodiversity and Community Analysis of Plant-Parasitic and Free-Living Nematodes Associated with Maize and Other Rotational Crops from Punjab, Pakistan. Life (Basel) 2021; 11:1426. [PMID: 34947957 DOI: 10.3390/life11121426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 01/13/2023] Open
Abstract
Maize (Zea mays L.) is one of Pakistan’s essential staple food crops. Plant-parasitic nematodes (PPNs) are a significant restraint in maize production. However, free-living nematodes (FLNs) provide crucial ecological functions such as suppressing pests and nutrient mineralization. This study aimed to assess the community analysis of plant-parasitic and free-living nematodes associated with maize and other rotational crops (those cultivated in sequence with the maize in the same field) from Punjab, Pakistan. The occurrence percentage was observed per 500 g soil for each nematode genus. The present study revealed that 24 species of plant-parasitic and free-living nematodes were identified from maize crops and other rotational crops from 16 localities through Punjab, Pakistan. Nematode communities were analyzed by absolute frequency, relative frequency, relative density, and prominence value, while cluster analysis was based on the presence or absence of nematode in different localities. The overall proportion of plant-parasitic nematodes was 35%, while free-living soil nematodes recovered 65%, out of 210 samples of maize and other rotational crops. Several major genera of plant-parasitic nematodes were reported during the present study viz., Ditylenchus, Filenchus, Helicotylenchus, Hemicriconemoides, Heterodera, Hoplolaimus, Malenchus, Pratylenchus, Psilenchus, Rotylenchulus, Seinura, Telotylenchus, Tylenchorhynchus, and Xiphinema Community relationship revealed the overall dominance of Heterodera zeae, with the highest incidence (55.71%) followed by Tylenchorhynchus elegans (33.33%) and Helicotylenchus certus (24.76%). The results provide valuable information on the community structure of nematodes in maize and other rotational crops of maize in Punjab, Pakistan. Moreover, this data can be used as a preventive measure before PPN incidence results in greater losses on maize.
Collapse
|
13
|
Okazaki K, Tsurumaru H, Hashimoto M, Takahashi H, Okubo T, Ohwada T, Minamisawa K, Ikeda S. Community Analysis-based Screening of Plant Growth-promoting Bacteria for Sugar Beet. Microbes Environ 2021; 36. [PMID: 33907063 PMCID: PMC8209457 DOI: 10.1264/jsme2.me20137] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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] [Indexed: 11/18/2022] Open
Abstract
Clone libraries of bacterial 16S rRNA genes (a total of 1,980 clones) were constructed from the leaf blades, petioles, taproots, and lateral roots of sugar beet (Beta vulgaris L.) grown under different fertilization conditions. A principal coordinate analysis revealed that the structures of bacterial communities in above- and underground tissues were largely separated by PC1 (44.5%). The bacterial communities of above-ground tissues (leaf blades and petioles) were more tightly clustered regardless of differences in the tissue types and fertilization conditions than those of below-ground tissues (taproots and lateral roots). The bacterial communities of below-ground tissues were largely separated by PC2 (26.0%). To survey plant growth-promoting bacteria (PGPBs), isolate collections (a total of 665 isolates) were constructed from the lateral roots. As candidate PGPBs, 44 isolates were selected via clustering analyses with the combined 16S rRNA gene sequence data of clone libraries and isolate collections. The results of inoculation tests using sugar beet seedlings showed that eight isolates exhibited growth-promoting effects on the seedlings. Among them, seven isolates belonging to seven genera (Asticcacaulis, Mesorhizobium, Nocardioides, Sphingobium, Sphingomonas, Sphingopyxis, and Polaromonas) were newly identified as PGPBs for sugar beet at the genus level, and two isolates belonging to two genera (Asticcacaulis and Polaromonas) were revealed to exert growth-promoting effects on the plant at the genus level for the first time. These results suggest that a community analysis-based selection strategy will facilitate the isolation of novel PGPBs and extend the potential for the development of novel biofertilizers.
Collapse
Affiliation(s)
- Kazuyuki Okazaki
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | | | | | - Hiroyuki Takahashi
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | | | - Takuji Ohwada
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine
| | | | - Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| |
Collapse
|
14
|
Solorzano L, Wik L, Olsson Bontell T, Wang Y, Klemm AH, Öfverstedt J, Jakola AS, Östman A, Wählby C. Machine learning for cell classification and neighborhood analysis in glioma tissue. Cytometry A 2021; 99:1176-1186. [PMID: 34089228 DOI: 10.1002/cyto.a.24467] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/28/2021] [Accepted: 05/25/2021] [Indexed: 12/21/2022]
Abstract
Multiplexed and spatially resolved single-cell analyses that intend to study tissue heterogeneity and cell organization invariably face as a first step the challenge of cell classification. Accuracy and reproducibility are important for the downstream process of counting cells, quantifying cell-cell interactions, and extracting information on disease-specific localized cell niches. Novel staining techniques make it possible to visualize and quantify large numbers of cell-specific molecular markers in parallel. However, due to variations in sample handling and artifacts from staining and scanning, cells of the same type may present different marker profiles both within and across samples. We address multiplexed immunofluorescence data from tissue microarrays of low-grade gliomas and present a methodology using two different machine learning architectures and features insensitive to illumination to perform cell classification. The fully automated cell classification provides a measure of confidence for the decision and requires a comparably small annotated data set for training, which can be created using freely available tools. Using the proposed method, we reached an accuracy of 83.1% on cell classification without the need for standardization of samples. Using our confidence measure, cells with low-confidence classifications could be excluded, pushing the classification accuracy to 94.5%. Next, we used the cell classification results to search for cell niches with an unsupervised learning approach based on graph neural networks. We show that the approach can re-detect specialized tissue niches in previously published data, and that our proposed cell classification leads to niche definitions that may be relevant for sub-groups of glioma, if applied to larger data sets.
Collapse
Affiliation(s)
- Leslie Solorzano
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Lina Wik
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Thomas Olsson Bontell
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Physiology, Institute of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Yuyu Wang
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Anna H Klemm
- Department of Information Technology, Uppsala University, Uppsala, Sweden.,BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
| | - Johan Öfverstedt
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Asgeir S Jakola
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Institute of Neuroscience and Physiology, Department of Clinical Neuroscience, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Arne Östman
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Carolina Wählby
- Department of Information Technology, Uppsala University, Uppsala, Sweden.,BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
| |
Collapse
|
15
|
Quaiyum S, Igarashi K, Narihiro T, Kato S. Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate. Microbes Environ 2020; 35. [PMID: 32921647 PMCID: PMC7511781 DOI: 10.1264/jsme2.me20002] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Methanogenic microbial communities were enriched from rice paddy soil and anaerobic digester sludge using peptidoglycan purified from gram-negative Escherichia coli or gram-positive Micrococcus luteus as the sole substrate. Methane production data suggested the anaerobic degradation of peptidoglycan and also that peptidoglycan from E. coli had lower degradability. The community structures of enrichment cultures fed peptidoglycan from E. coli or M. luteus were similar, but distinctly different. A number of phylogenetically novel and uncultured bacteria, particularly in the phyla Bacteroidetes, WWE1, Armatimonadetes, and Verrucomicrobia, dominated the enrichment cultures, suggesting their involvement in anaerobic peptidoglycan degradation.
Collapse
Affiliation(s)
- Samia Quaiyum
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| |
Collapse
|
16
|
Henneghan A, Wright ML, Bourne G, Sales AC. A Cross-Sectional Exploration of Cytokine-Symptom Networks in Breast Cancer Survivors Using Network Analysis. Can J Nurs Res 2020; 53:303-315. [PMID: 32482100 DOI: 10.1177/0844562120927535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The purpose of this study is to (a) visualize the symptom-cytokine networks (perceived stress, fatigue, loneliness, perceived cognitive impairment, daytime sleepiness, sleep quality, and 13 cytokines) and (b) explore centrality metrics of symptom-cytokine networks in breast cancer survivors who completed chemotherapy treatment. METHODS Cross-sectional analysis of data collected from 66 breast cancer survivors who were on average three years post chemotherapy completion. Perceived stress, fatigue, loneliness, perceived cognitive impairment, daytime sleepiness, and sleep quality were measured with self-report instruments, and a panel of 13 cytokines was measured from serum using multiplex assays. Symptoms and cytokines were simultaneously evaluated with correlations, network analysis, and community analysis. RESULTS Network analysis revealed the nodes with the greatest degree and closeness were interleukin-2, granulocyte-macrophage colony-stimulating factor, interleukin-13, and perceived cognitive impairment. Node betweenness was highest for perceived cognitive impairment and interleukin-2. Community analysis revealed two separate communities of nodes within the network (symptoms and the cytokines). Several edges connected the two communities including perceived cognitive impairment, stress, fatigue, depression, interleukin-2, granulocyte-macrophage colony-stimulating factor, interleukin-8, interleukin-13, and interleukin-10. Partial correlation analyses revealed significant negative relationships between interleukin-2 and fatigue, loneliness, stress, and perceived cognitive impairment (rs = -.27 to -.37, ps < .05) and a significant negative relationship between perceived cognitive impairment and granulocyte-macrophage colony-stimulating factor (r = -.34, p < .01). CONCLUSIONS Our analyses support that perceived cognitive impairment, stress, loneliness, depressive symptoms, and fatigue co-occur and extend the literature by suggesting that interleukin-2 may contribute to the underlying mechanistic pathway of these co-occurring symptoms. Our findings add to a growing body of literature that is shifting to study symptoms as they co-occur, or cluster, rather than individual symptoms.
Collapse
Affiliation(s)
- Ashley Henneghan
- Livestrong Cancer Institute, School of Nursing, University of Texas at Austin, Austin, TX, USA
| | - Michelle L Wright
- School of Nursing, Dell Medical School, University of Texas at Austin, Austin, TX, USA.,Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Garrett Bourne
- Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Adam C Sales
- Statistics, Measurement, and Research Design Techniques in Educational Research, University of Texas at Austin College of Education, Austin, TX, USA
| |
Collapse
|
17
|
Ruggiero A, Grattepanche JD, Weiner AKM, Katz LA. High Diversity of Testate Amoebae (Amoebozoa, Arcellinida) Detected by HTS Analyses in a New England Fen using Newly Designed Taxon-specific Primers. J Eukaryot Microbiol 2020; 67:450-462. [PMID: 32145128 DOI: 10.1111/jeu.12794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 01/01/2023]
Abstract
Testate (shell-building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida-specific primers for the SSU-rDNA gene to assess the community composition on the molecular level in a pilot study of two samplings from a New England fen: (1) 36-cm horizontal transects and vertical cores; and (2) 26-m horizontal transects fractioned into four size classes (2-10, 10-35, 35-100, and 100-300 μm). Analyses of these data show the following: (1) a considerable genetic diversity within Arcellinida, much of which comes from morphospecies lacking sequences on GenBank; (2) communities characterized by DNA (i.e. active + quiescent) are distinct from those characterized by RNA (i.e. active, indicator of biomass); (3) active communities on the surface tend to be more similar to one another than to core communities, despite considerable heterogeneity; and (4) analyses of communities fractioned by size find some lineages (OTUs) that are abundant in disjunct size categories, suggesting the possibility of life-history stages. Together, these data demonstrate the potential of these primers to elucidate the diversity of Arcellinida communities in diverse habitats.
Collapse
Affiliation(s)
- Alistaire Ruggiero
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Jean-David Grattepanche
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Agnes K M Weiner
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Laura A Katz
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| |
Collapse
|
18
|
Pellegrino E, Gamper HA, Ciccolini V, Ercoli L. Forage Rotations Conserve Diversity of Arbuscular Mycorrhizal Fungi and Soil Fertility. Front Microbiol 2020; 10:2969. [PMID: 31998261 PMCID: PMC6962183 DOI: 10.3389/fmicb.2019.02969] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/09/2019] [Indexed: 01/07/2023] Open
Abstract
In the Mediterranean, long-term impact of typical land uses on soil fertility have not been quantified yet on replicated mixed crop-livestock farms and considering the variability of soil texture. Here, we report the effects, after 15 years of practice, of two legume-winter cereal rotations, olive orchards and vineyards on microbiological and chemical indicators of soil fertility and the communities of arbuscular mycorrhizal fungi (AMF). We compare the changes among these four agricultural land-use types to woodland reference sites. Root colonization by AMF of English ryegrass (Lolium perenne L.), a grass that occurred under all land use types, was only half as heavy in biannual berseem clover (Trifolium alexandrinum L.)-winter cereal rotations than in 4-year alfalfa (Medicago sativa L.)-winter cereal rotations. In olive (Olea europaea L.) orchards and vineyards (Vitis vinifera L.), where weeds are controlled by frequent surface tillage, the AMF root colonization of ryegrass was again much lower than in the legume-cereal rotations and at the woodland reference sites. All the microbial parameters and soil organic carbon correlated most strongly with differences in occurrence and relative abundance (β-diversity) of AMF genera in soil. The soil pH and mineral nutrients in soil strongly correlated with differences in AMF root colonization and AMF genus richness (α-diversity) in soil. Diversity of AMF was much less affected by soil texture than land use, while the opposite was true for microbial and chemical soil fertility indicators. Land uses that guaranteed a continuous ground cover of herbaceous plants and that involved only infrequent tillage, such as multiyear alfalfa-winter cereal rotation, allowed members of the AMF genus Scutellospora to persist and remain abundant. On the contrary, under land uses accompanied by frequent tillage and hence discontinuous presence of herbaceous plants, such as tilled olive orchard and vineyard, members of the genus Funneliformis dominated. These results suggest that multiyear alfalfa-winter cereal rotation with active plant growth throughout the year is the least detrimental agricultural land use in soil carbon and AMF abundance and diversity, relative to the woodland reference.
Collapse
Affiliation(s)
- Elisa Pellegrino
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Hannes A. Gamper
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | | | - Laura Ercoli
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| |
Collapse
|
19
|
Lee DY, Lee DS, Bae MJ, Hwang SJ, Noh SY, Moon JS, Park YS. Distribution Patterns of Odonate Assemblages in Relation to Environmental Variables in Streams of South Korea. Insects 2018; 9:E152. [PMID: 30380629 DOI: 10.3390/insects9040152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/16/2022]
Abstract
Odonata species are sensitive to environmental changes, particularly those caused by humans, and provide valuable ecosystem services as intermediate predators in food webs. We aimed: (i) to investigate the distribution patterns of Odonata in streams on a nationwide scale across South Korea; (ii) to evaluate the relationships between the distribution patterns of odonates and their environmental conditions; and (iii) to identify indicator species and the most significant environmental factors affecting their distributions. Samples were collected from 965 sampling sites in streams across South Korea. We also measured 34 environmental variables grouped into six categories: geography, meteorology, land use, substrate composition, hydrology, and physicochemistry. A total of 83 taxa belonging to 10 families of Odonata were recorded in the dataset. Among them, eight species displayed high abundances and incidences. Self-organizing map (SOM) classified sampling sites into seven clusters (A⁻G) which could be divided into two distinct groups (A⁻C and D⁻G) according to the similarities of their odonate assemblages. Clusters A⁻C were characterized by members of the suborder Anisoptera, whereas clusters D⁻G were characterized by the suborder Zygoptera. Non-metric multidimensional scaling (NMDS) identified forest (%), altitude, and cobble (%) in substrata as the most influential environmental factors determining odonate assemblage compositions. Our results emphasize the importance of habitat heterogeneity by demonstrating its effect on odonate assemblages.
Collapse
|
20
|
Yang H, Xu F, Meng C, Su S, Yuan X. [Rapid Improvement of Denitrification Performance of Embedded Activated Sludge and Community Analysis]. Huan Jing Ke Xue 2018; 39:4661-4669. [PMID: 30229615 DOI: 10.13227/j.hjkx.201801064] [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] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The purpose of this study was to rapidly improve the denitrification packing activity in the denitrification pond sludge of sewage plants, to realize the engineering application of embedding immobilization, and to explore the characteristics of the microbial community of the embedding packing. The effects of different C/N ratios, temperature, and pH on the activity of embedding filler were studied by batch experiments, and the biological community characteristics of embedding filler were studied by high-throughput sequencing. Results showed that the embedding packing in C/N to 10, the temperature of 30℃, and pH of 7.5±0.3, resumed 5.37 mg·(g·h)-1 of the initial activity after 7 days. Under the optimized culture conditions of C/N ratio of 10, temperature of 25℃, and pH of 8.0, the specific rate of denitrification can be increased by 15 times to 80.17 mg·(g·h)-1 after 15 days, and stabilized at that level. SEM results showed that there were a large number of mass transfer channels inside the embedding fillers, and that the bacteria grew well as clusters in the encapsulated fillers. The high throughput sequencing showed that the denitrifying function of Thauera and Thermomonas were 24.27% and 8.23% respectively, which ensured the high efficiency of denitrifying nitrogen removal. The rapid proliferation of Thauera dominant bacteria and Thermomonas under optimal culture conditions was the main reason for the rapid increase of packing activity.
Collapse
Affiliation(s)
- Hong Yang
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
| | - Fu Xu
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
| | - Chen Meng
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
| | - Shan Su
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xing Yuan
- Beijing Drainage Group Co., Ltd., Beijing 100124, China
| |
Collapse
|
21
|
Vandenbroucke L, Weeda W, Lee N, Baeyens D, Westfall J, Figner B, Huizinga M. Heterogeneity in Cognitive and Socio-Emotional Functioning in Adolescents With On-Track and Delayed School Progression. Front Psychol 2018; 9:1572. [PMID: 30197618 PMCID: PMC6118220 DOI: 10.3389/fpsyg.2018.01572] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/07/2018] [Indexed: 02/03/2023] Open
Abstract
Adolescence is characterized by considerable changes in cognitive and socio-emotional skills. There are considerable differences between adolescents with regards to the development of these skills. However, most studies examine adolescents' average functioning, without taking into account this heterogeneity. The current study applies network analysis in order to examine heterogeneity of cognitive and socio-emotional functioning in adolescents on-track or delayed in their school progression. Data was collected at two time-points for on-track (n = 320) and delayed (n = 69) adolescents (Mage = 13.30 years, SDage = 0.77). Repeated measures ANOVA showed no significant differences between the groups in cognitive and socio-emotional functioning (p's > 0.05). Network analysis revealed that executive functions play a key role in the network of cognitive, social, and emotional functioning. This is especially the case in the delayed group where executive functions are even more central, both at T1 (inhibition and shifting) and T2 (shifting). Subsequent community analysis revealed three profiles in both groups: a well-adapted and well-balanced group, a group with high levels of need for arousal and risk-taking, and a group with regulation problems. Compared to on-track adolescents, delayed adolescents showed even higher levels of risk-taking in the second profile and higher levels of executive function problems in the third profile at T1. These differences were leveled out at T2, indicating adolescents in the delayed group catch up with their peers. This study highlights the intricate balance between cognitive, social and emotional functioning in adolescents in relation to school performance and provides preliminary evidence of the importance of taking individual differences within groups into account.
Collapse
Affiliation(s)
- Loren Vandenbroucke
- Research Group of Parenting and Special Education, KU Leuven, Leuven, Belgium
| | - Wouter Weeda
- Department of Methodology and Statistics, Leiden University, Leiden, Netherlands
| | - Nikki Lee
- Department of Clinical, Neuro- and Developmental Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Dieter Baeyens
- Research Group of Parenting and Special Education, KU Leuven, Leuven, Belgium
| | - Jon Westfall
- Department of Counselor Education and Psychology, Delta State University, Cleveland, MS, United States
| | - Bernd Figner
- Behavioural Science Institute, Radboud University, Nijmegen, Netherlands
| | - Mariëtte Huizinga
- Department of Educational and Family Studies, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
22
|
BURLAKOVA LYUBOVE, BARBIERO RICHARDP, KARATAYEV ALEXANDERY, DANIEL SUSANE, HINCHEY ELIZABETHK, WARREN GLENNJ. The benthic community of the Laurentian Great Lakes: analysis of spatial gradients and temporal trends from 1998-2014. J Great Lakes Res 2018; 44:600-617. [PMID: 31031520 PMCID: PMC6483096 DOI: 10.1016/j.jglr.2018.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We used the results of seventeen years of Great Lakes benthic monitoring conducted by the U.S. EPA's Great Lakes National Program Office to describe the spatial and temporal patterns of benthic communities, assess their status, trends, and main drivers, and to infer the potential impact of these community changes on ecosystem functioning. Benthic abundance and diversity were higher at shallow (<70 m in depth) stations with chlorophyll concentrations above 3 μg/L than at deeper sites (<1 μg/L).We infer that lake productivity, measured by chlorophyll was likely the major driver of benthic abundance and diversity across lakes. Consequently, benthic diversity and abundance were the highest in the most productive Lake Erie, followed by lakes Ontario, Michigan, Huron, and Superior. Multivariate analysis distinguished three major communities shared among lakes (littoral, sublittoral, and profundal) that differed in species composition and abundance, functional group diversity, and tolerance to organic pollution. Analysis of temporal trends revealed that the largest changes occurred in profundal communities, apparent in significant shifts in dominant taxa across all lakes except Lake Superior. In lakes Michigan, Huron, and Ontario, the former dominant Diporeia was replaced with Dreissena and Oligochaeta. Profundal species, with the exception of dreissenids, became less abundant, and their depth distribution has shifted. In contrast, density and diversity of native littoral and sublittoral communities increased. The invasion of dreissenids was among the most important drivers of changes in benthic communities. Continued monitoring is critical for tracking unprecedented changes occurring in the Great Lakes ecosystem.
Collapse
Affiliation(s)
- LYUBOV E. BURLAKOVA
- Great Lakes Center, Buffalo State College, 1300 Elmwood Ave., Buffalo, NY 14222, USA. Phone: 716-878-4504, Fax: 716-878-6644
| | - RICHARD P. BARBIERO
- CSRA, 1359 W. Elmdale Ave. Suite 2, Chicago, IL 60660, USA. Phone: 773-878-3661
| | - ALEXANDER Y. KARATAYEV
- Great Lakes Center, Buffalo State College, 1300 Elmwood Ave., Buffalo, NY 14222, USA. Phone: 716-878-4504, Fax: 716-878-6644
| | - SUSAN E. DANIEL
- Great Lakes Center, Buffalo State College, 1300 Elmwood Ave., Buffalo, NY 14222, USA. Phone: 716-878-4504, Fax: 716-878-6644
| | - ELIZABETH K. HINCHEY
- United States Environmental Protection Agency, Great Lakes National Program Office, Chicago, Illinois, USA. Phone: 312-886-3451, 312-886-2405
| | - GLENN J. WARREN
- United States Environmental Protection Agency, Great Lakes National Program Office, Chicago, Illinois, USA. Phone: 312-886-3451, 312-886-2405
| |
Collapse
|
23
|
Koeller K, Herlemann DPR, Schuldt T, Ovari A, Guder E, Podbielski A, Kreikemeyer B, Olzowy B. Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa. Front Microbiol 2018; 9:643. [PMID: 29755418 PMCID: PMC5932350 DOI: 10.3389/fmicb.2018.00643] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/19/2018] [Indexed: 12/18/2022] Open
Abstract
The role of bacteria in chronic rhinosinusitis (CRS) is still not well understood. Whole microbiome analysis adds new aspects to our current understanding that is mainly based on isolated bacteria. It is still unclear how the results of microbiome analysis and the classical culture based approaches interrelate. To address this, middle meatus swabs and tissue samples were obtained during sinus surgery in 5 patients with CRS with nasal polyps (CRSwNP), 5 patients with diffuse CRS without nasal polyps (CRSsNP), 5 patients with unilateral purulent maxillary CRS (upm CRS) and 3 patients with healthy sinus mucosa. Swabs were cultured, and associated bacteria were identified. Additionally, parts of each tissue sample also underwent culture approaches, and in parallel DNA was extracted for 16S rRNA gene amplicon-based microbiome analysis. From tissue samples 4.2 ± 1.2 distinct species per patient were cultured, from swabs 5.4 ± 1.6. The most frequently cultured species from the swabs were Propionibacterium acnes, Staphylococcus epidermidis, Corynebacterium spp. and Staphylococcus aureus. The 16S-RNA gene analysis revealed no clear differentiation of the bacterial community of healthy compared to CRS samples of unilateral purulent maxillary CRS and CRSwNP. However, the bacterial community of CRSsNP differed significantly from the healthy controls. In the CRSsNP samples Flavobacterium, Pseudomonas, Pedobacter, Porphyromonas, Stenotrophomonas, and Brevundimonas were significantly enriched compared to the healthy controls. Species isolated from culture did not generally correspond with the most abundant genera in microbiome analysis. Only Fusobacteria, Parvimonas, and Prevotella found in 2 unilateral purulent maxillary CRS samples by the cultivation dependent approach were also found in the cultivation independent approach in high abundance, suggesting a classic infectious pathogenesis of odontogenic origin in these two specific cases. Alterations of the bacterial community might be a more crucial factor for the development of CRSsNP compared to CRSwNP. Further studies are needed to investigate the relation between bacterial community characteristics and the development of CRSsNP.
Collapse
Affiliation(s)
- Kerstin Koeller
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Daniel P R Herlemann
- Biological Oceanography Section, Leibniz Institute for Baltic Sea Research, Warnemünde, Rostock, Germany.,Center of Limnology, Estonian University of Life Sciences, Tartu, Estonia
| | - Tobias Schuldt
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Rostock, Rostock, Germany
| | - Attila Ovari
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Rostock, Rostock, Germany
| | - Ellen Guder
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Rostock, Rostock, Germany
| | - Andreas Podbielski
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Bernhard Olzowy
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Rostock, Rostock, Germany.,HNO-Zentrum Landsberg, Landsberg am Lech, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University of Munich Medical Center, Munich, Germany
| |
Collapse
|
24
|
Kerwin AH, Nyholm SV. Reproductive System Symbiotic Bacteria Are Conserved between Two Distinct Populations of Euprymna scolopes from Oahu, Hawaii. mSphere 2018; 3:e00531-17. [PMID: 29600280 DOI: 10.1128/mSphere.00531-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/26/2018] [Indexed: 02/04/2023] Open
Abstract
In this study, we examined the reproductive ANG symbiosis found in two genetically isolated populations of the Hawaiian bobtail squid, Euprymna scolopes. The stability of the community reported here provides support for the hypothesis that this symbiosis is under strong selective pressure, while the observed differences suggest that some level of local adaptation may have occurred. These two host populations are frequently used interchangeably as source populations for research. Euprymna scolopes is an important model organism and offers the opportunity to examine the interplay between a binary and a consortial symbiosis in a single model host. Understanding the inherent natural variability of this association will aid in our understanding of the conservation, function, transmission, and development of the ANG symbiosis. Female Hawaiian bobtail squid, Euprymna scolopes, harbor a symbiotic bacterial community in a reproductive organ, the accessory nidamental gland (ANG). This community is known to be stable over several generations of wild-caught bobtail squid but has, to date, been examined for only one population in Maunalua Bay, Oahu, HI. This study assessed the ANG and corresponding egg jelly coat (JC) bacterial communities for another genetically isolated host population from Kaneohe Bay, Oahu, HI, using 16S amplicon sequencing. The bacterial communities from the ANGs and JCs of the two populations were found to be similar in richness, evenness, phylogenetic diversity, and overall community composition. However, the Kaneohe Bay samples formed their own subset within the Maunalua Bay ANG/JC community. An Alteromonadaceae genus, BD2-13, was significantly higher in relative abundance in the Kaneohe Bay population, and several Alphaproteobacteria taxa also shifted in relative abundance between the two groups. This variation could be due to local adaptation to differing environmental challenges, to localized variability, or to functional redundancy among the ANG taxa. The overall stability of the community between the populations further supports a crucial functional role that has been hypothesized for this symbiosis. IMPORTANCE In this study, we examined the reproductive ANG symbiosis found in two genetically isolated populations of the Hawaiian bobtail squid, Euprymna scolopes. The stability of the community reported here provides support for the hypothesis that this symbiosis is under strong selective pressure, while the observed differences suggest that some level of local adaptation may have occurred. These two host populations are frequently used interchangeably as source populations for research. Euprymna scolopes is an important model organism and offers the opportunity to examine the interplay between a binary and a consortial symbiosis in a single model host. Understanding the inherent natural variability of this association will aid in our understanding of the conservation, function, transmission, and development of the ANG symbiosis.
Collapse
|
25
|
Affiliation(s)
- Lauren C Cline
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Zewei Song
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - Gabriel A Al-Ghalith
- Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Dan Knights
- Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| |
Collapse
|
26
|
Noune C, Hauxwell C. MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data. Biology (Basel) 2017; 6:E14. [PMID: 28218638 DOI: 10.3390/biology6010014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/06/2017] [Accepted: 02/07/2017] [Indexed: 02/01/2023]
Abstract
Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of ‘meta-barcode’ data. This approach relies on comparison of amplicon sequences of ‘barcode’ regions from a population with public-domain databases of reference sequences. However, for many organisms relevant ‘barcode’ regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, ‘MetaGaAP,’ was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom ‘barcode’ regions of less than 30 polymorphisms within the span of a single ‘read’, amplification and sequencing of the ‘barcode’, generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes. The pipeline and workflow were validated in a ‘wild type’ Alphabaculovirus isolate, Helicoverpa armigera single nucleopolyhedrovirus (HaSNPV-AC53) and a tissue-culture derived strain (HaSNPV-AC53-T2). The approach was validated by comparison of polymorphisms in amplicons and shotgun data, and by comparison of predicted dominant and co-dominant genotypes with Sanger sequences. The computational power required to generate and search the database effectively limits the number of polymorphisms that can be included in a barcode to 30 or less. The approach can be used in quantitative analysis of the ecology and pathology of non-model organisms.
Collapse
|
27
|
Johannesen J. Tracing the history and ecological context of Wolbachia double infection in a specialist host ( Urophora cardui)-parasitoid ( Eurytoma serratulae) system. Ecol Evol 2017; 7:986-996. [PMID: 28168034 PMCID: PMC5288247 DOI: 10.1002/ece3.2713] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 06/09/2016] [Revised: 11/24/2016] [Accepted: 12/17/2016] [Indexed: 12/03/2022] Open
Abstract
The endosymbiotic bacterium Wolbachia is the most widespread bacteria in insects, yet the ecology of novel acquisitions in natural host populations is poorly understood. Using temporal data separated by 12 years, I tested the hypothesis that immigration of a parasitoid wasp led to transmission of its Wolbachia strain to its dipteran host, resulting in double‐strain infection, and I used geographic and community surveys to explore the history of transmission in fly and parasitoid. Double infection in the fly host was present before immigration of the parasitoid. Equal prevalence of double infection in males and females, constant prevalence before and after immigration in two regions, and increase in one region of immigration indicate little if no competition between strains. Double infection was present throughout the fly's distribution range, but proportions varied highly (0–0.71, mean = 0.26). Two fly‐specific MLST strains, observed in Eastern and Western Europe, respectively, differed at hcpA only. Flies with either fly‐strain could be double infected with the parasitoid's strain. The geographic distribution of double infection implies that it is older than the fly host's extent distribution range and that different proportions of double infection are caused by demographic fluctuations in the fly. The geographic data in combination with community surveys of infections and strains further suggest that the parasitoid strain was the fly's ancestral strain that was transmitted to the parasitoid, that is, the reverse transmission route as first hypothesized. Based on these findings together with a comparison of oviposition strategies of other hosts harboring related Wolbachia strains, I hypothesize that trans‐infection during an insect host's puparial metamorphosis might be important in promoting horizontal transmission among diverse holometabolic taxa.
Collapse
Affiliation(s)
- Jes Johannesen
- Department of Evolutionary Ecology Zoological Institute University of Mainz Mainz Germany
| |
Collapse
|
28
|
Zhao J, Nussinov R, Ma B. Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains. Protein Eng Des Sel 2017; 30:67-76. [PMID: 27899437 PMCID: PMC5157118 DOI: 10.1093/protein/gzw065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 06/01/2016] [Revised: 10/05/2016] [Accepted: 11/14/2016] [Indexed: 12/12/2022] Open
Abstract
Molecular details of the recognition of disordered antigens by their cognate antibodies have not been studied as extensively as folded protein antigens and much is still unknown. To follow the conformational changes in the antibody and cross-talk between its subunits and with antigens, we performed molecular dynamics (MD) simulations of the complex of Fab and prion-associated peptide in the apo and bound forms. We observed that the inter-chain disulfide bond in constant domains restrains the conformational changes of Fab, especially the loops in the CH1 domain, resulting in inhibition of the cross-talk between Fab subdomains that thereby may prevent prion peptide binding. We further identified several negative and positive correlations of motions between the peptide and Fab constant domains, which suggested structural cross-talks between the constant domains and the antigen. The cross-talk was influenced by the inter-chain disulfide bond, which reduced the number of paths between them. Importantly, network analysis of the complex and its bound water molecules observed that those water molecules form an integral part of the Fab/peptide complex network and potential allosteric pathways. On-going work focuses on developing strategies aimed to incorporate these new network communications-including the associated water molecules-toward the grand challenge of antibody design.
Collapse
Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Genetics and Molecular Medicine, Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| |
Collapse
|
29
|
Lv X, Liu H, Chen H, Gong H. Coupling between ATP hydrolysis and protein conformational change in maltose transporter. Proteins 2016; 85:207-220. [PMID: 27616441 DOI: 10.1002/prot.25160] [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] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/29/2016] [Accepted: 09/02/2016] [Indexed: 11/12/2022]
Abstract
As the intracellular part of maltose transporter, MalK dimer utilizes the energy of ATP hydrolysis to drive protein conformational change, which then facilitates substrate transport. Free energy evaluation of the complete conformational change before and after ATP hydrolysis is helpful to elucidate the mechanism of chemical-to-mechanical energy conversion in MalK dimer, but is lacking in previous studies. In this work, we used molecular dynamics simulations to investigate the structural transition of MalK dimer among closed, semi-open and open states. We observed spontaneous structural transition from closed to open state in the ADP-bound system and partial closure of MalK dimer from the semi-open state in the ATP-bound system. Subsequently, we calculated the reaction pathways connecting the closed and open states for the ATP- and ADP-bound systems and evaluated the free energy profiles along the paths. Our results suggested that the closed state is stable in the presence of ATP but is markedly destabilized when ATP is hydrolyzed to ADP, which thus explains the coupling between ATP hydrolysis and protein conformational change of MalK dimer in thermodynamics. Proteins 2017; 85:207-220. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Xiaoying Lv
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hao Liu
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial metabolism, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Haifeng Chen
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial metabolism, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
30
|
Abstract
The use of antibiotics in aquaculture raises environmental and food safety concerns because chronic exposure of an aquatic ecosystem to antibiotics can result in the spread of antibiotic resistance, bioaccumulation of antibiotics in the organisms, and transfer of antibiotics to humans. In an attempt to overcome these problems, high-concentration red clay was applied as an alternative antibiotic against the following common fish pathogens: Aeromonas salmonicida, Vibrio alginolyticus, and Streptococcus equinus. The growth of A. salmonicida and V. alginolyticus was retarded by red clay, whereas that of S. equinus was promoted. Phase contrast and scanning electron microscopy analyses confirmed the attachment of red clay on cell surfaces, resulting in rapid gravitational removal and cell surface damage in both A. salmonicida and V. alginolyticus, but not in S. equinus. Different cell wall properties of grampositive species may explain the unharmed cell surface of S. equinus. Significant levels of oxidative stress were generated in only the former two species, whereas significant changes in membrane permeability were found only in S. equinus, probably because of its physiological adaptation. The bacterial communities in water samples from Oncorhynchus mykiss aquacultures supplemented with red clay showed similar structure and diversity as those from oxytetracycline-treated water. Taken together, the antibiotic effects of high concentrations of red clay in aquaculture can be attributed to gravitational removal, cell surface damage, and oxidative stress production, and suggest that red clay may be used as an alternative for antibiotics in aquaculture.
Collapse
Affiliation(s)
- Jaejoon Jung
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Seung Cheol Jee
- Department of Life Science, Dongguk University, Seoul, 04620, Republic of Korea
| | - Jung-Suk Sung
- Department of Life Science, Dongguk University, Seoul, 04620, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| |
Collapse
|
31
|
Guo C, Zhou HX. Unidirectional allostery in the regulatory subunit RIα facilitates efficient deactivation of protein kinase A. Proc Natl Acad Sci U S A 2016; 113:E6776-85. [PMID: 27791125 DOI: 10.1073/pnas.1610142113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The holoenzyme complex of protein kinase A is in an inactive state; activation involves ordered cAMP binding to two tandem domains of the regulatory subunit and release of the catalytic subunit. Deactivation has been less studied, during which the two cAMPs unbind from the regulatory subunit to allow association of the catalytic subunit to reform the holoenzyme complex. Unbinding of the cAMPs appears ordered as indicated by a large difference in unbinding rates from the two sites, but the cause has remained elusive given the structural similarity of the two tandem domains. Even more intriguingly, NMR data show that allosteric communication between the two domains is unidirectional. Here, we present a mechanism for the unidirectionality, developed from extensive molecular dynamics simulations of the tandem domains in different cAMP-bound forms. Disparate responses to cAMP releases from the two sites (A and B) in conformational flexibility and chemical shift perturbation confirmed unidirectional allosteric communication. Community analysis revealed that the A-site cAMP, by forming across-domain interactions, bridges an essential pathway for interdomain communication. The pathway is impaired when this cAMP is removed but remains intact when only the B-site cAMP is removed. Specifically, removal of the A-site cAMP leads to the separation of the two domains, creating room for binding the catalytic subunit. Moreover, the A-site cAMP, by maintaining interdomain coupling, retards the unbinding of the B-site cAMP and stalls an unproductive pathway of cAMP release. Our work expands the perspective on allostery and implicates functional importance for the directionality of allostery.
Collapse
|
32
|
Wheelock MJ, Rey KP, O'Neal ME. Defining the Insect Pollinator Community Found in Iowa Corn and Soybean Fields: Implications for Pollinator Conservation. Environ Entomol 2016; 45:1099-1106. [PMID: 27516433 DOI: 10.1093/ee/nvw087] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 09/02/2015] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
Although corn (Zea mays L.) and soybeans (Glycine max L.) do not require pollination, they offer floral resources used by insect pollinators. We asked if a similar community of insect pollinators visits these crops in central Iowa, a landscape dominated by corn and soybean production. We used modified pan traps (i.e., bee bowls) in both corn and soybean fields during anthesis and used nonmetric multidimensional scaling (NMS) to compare the communities found in the two crops. Summed across both crops, 6,704 individual insects were captured representing at least 60 species, morphospecies, or higher-level taxa. Thirty-four species were collected in both crops, 19 collected only in corn and seven were collected only in soybean. The most abundant taxa were Lasioglossum [Dialictus] spp., Agapostemon virescens Cresson, Melissodes bimaculata (Lepeletier), and Toxomerus marginatus (Say), which accounted for 65% of the insect pollinators collected from both crops. Although social bees (Apis mellifera L. and Bombus spp.) were found in both crops, they accounted for only 0.5% of all insects captured. The NMS analysis revealed a shared community of pollinators composed of mostly solitary, ground nesting bees. Many of these species have been found in other crop fields throughout North America. Although corn and soybean are grown in landscapes that are often highly disturbed, these data suggest that a community of pollinators can persist within them. We suggest approaches to conserving this community based on partnering with activities that aim to lessen the environmental impact of annual crop production.
Collapse
Affiliation(s)
- M J Wheelock
- Department of Entomology, Iowa State University, Ames, IA 50011 (; )
| | - K P Rey
- Department of Statistics, Iowa State University, Ames, IA 50011
| | - M E O'Neal
- Department of Entomology, Iowa State University, Ames, IA 50011 (; )
| |
Collapse
|
33
|
Abstract
Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities.
Collapse
Affiliation(s)
- Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| |
Collapse
|
34
|
Abstract
High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or OTU composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests and nonparametric testing using community networks and the ggnetwork package.
Collapse
Affiliation(s)
- Ben J Callahan
- Statistics Department, Stanford University, Stanford, CA, 94305, USA
| | - Kris Sankaran
- Statistics Department, Stanford University, Stanford, CA, 94305, USA
| | - Julia A Fukuyama
- Statistics Department, Stanford University, Stanford, CA, 94305, USA
| | | | - Susan P Holmes
- Statistics Department, Stanford University, Stanford, CA, 94305, USA
| |
Collapse
|
35
|
Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses. F1000Res 2016; 5:1492. [PMID: 27508062 DOI: 10.12688/f1000research.8986.1] [Citation(s) in RCA: 284] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 11/20/2022] Open
Abstract
High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or OTU composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests and nonparametric testing using community networks and the ggnetwork package.
Collapse
Affiliation(s)
- Ben J Callahan
- Statistics Department, Stanford University, Stanford, CA, 94305, USA
| | - Kris Sankaran
- Statistics Department, Stanford University, Stanford, CA, 94305, USA
| | - Julia A Fukuyama
- Statistics Department, Stanford University, Stanford, CA, 94305, USA
| | | | - Susan P Holmes
- Statistics Department, Stanford University, Stanford, CA, 94305, USA
| |
Collapse
|
36
|
Lin S, Vasseur L, You MS. Seasonal Variability in Spider Assemblages in Traditional and Transgenic Rice Fields. Environ Entomol 2016; 45:537-546. [PMID: 26856757 DOI: 10.1093/ee/nvw002] [Citation(s) in RCA: 2] [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: 06/17/2015] [Accepted: 01/11/2016] [Indexed: 06/05/2023]
Abstract
The use of Bt transgenic rice (or Bt rice) remains controversial in several countries, including China. Risk assessments are a prerequisite to confirm the safety of Bt rice for ecosystems before a commercial release. This study was conducted to compare the responses of spider assemblages to Bt rice and nontransgenic rice. Two experiments with different locations and times were conducted, and the data were analyzed using standard diversity indices and multivariate community analysis. With both analytical approaches, spider diversity and assemblage composition were not significantly different between Bt and non transgenic rice fields. However, based on principal component analyses, temporal (seasonal) variations occurred in the composition of the spider assemblage. In this study, Bt rice had no detrimental effects on the spider assemblages, although assemblage composition and species abundance varied during the growing season. This study demonstrated an advantage in using community assemblages and repeated sampling to compare fields over a growing season because changes in the assemblages, and more specifically for some species, not always the most dominant, may vary over time. To more accurately assess the changes in composition and structure of spider assemblages through time, particularly for those species that may require a longer period to detect a response, an increase in sampling effort and longer-term experiments might be required.
Collapse
Affiliation(s)
- Sheng Lin
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou 350002, China, Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou 350002, China, Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, China, Fuzhou 350002, China, Fujian Provincial Key Laboratory of Insect Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China, Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Liette Vasseur
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou 350002, China, Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, China, Fuzhou 350002, China, Fujian Provincial Key Laboratory of Insect Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China, Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Min-Sheng You
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou 350002, China, Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou 350002, China, Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, China, Fuzhou 350002, China, Fujian Provincial Key Laboratory of Insect Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China,
| |
Collapse
|
37
|
Abstract
Protein kinases have very dynamic structures and their functionality strongly depends on their dynamic state. Active kinases reveal a dynamic pattern with residues clustering into semirigid communities that move in μs-ms timescale. Previously detected hydrophobic spines serve as connectors between communities. Communities do not follow the traditional subdomain structure of the kinase core or its secondary structure elements. Instead they are organized around main functional units. Integration of the communities depends on the assembly of the hydrophobic spine and phosphorylation of the activation loop. Single mutations can significantly disrupt the dynamic infrastructure and thereby interfere with long-distance allosteric signaling that propagates throughout the whole molecule. Dynamics is proposed to be the underlying mechanism for allosteric regulation in protein kinases.
Collapse
Affiliation(s)
- Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA, 92093, USA.
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA, 92093, USA; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
38
|
Abstract
Protein kinases are dynamically regulated signaling proteins that act as switches in the cell by phosphorylating target proteins. To establish a framework for analyzing linkages between structure, function, dynamics, and allostery in protein kinases, we carried out multiple microsecond-scale molecular-dynamics simulations of protein kinase A (PKA), an exemplar active kinase. We identified residue-residue correlated motions based on the concept of mutual information and used the Girvan-Newman method to partition PKA into structurally contiguous "communities." Most of these communities included 40-60 residues and were associated with a particular protein kinase function or a regulatory mechanism, and well-known motifs based on sequence and secondary structure were often split into different communities. The observed community maps were sensitive to the presence of different ligands and provide a new framework for interpreting long-distance allosteric coupling. Communication between different communities was also in agreement with the previously defined architecture of the protein kinase core based on the "hydrophobic spine" network. This finding gives us confidence in suggesting that community analyses can be used for other protein kinases and will provide an efficient tool for structural biologists. The communities also allow us to think about allosteric consequences of mutations that are linked to disease.
Collapse
|
39
|
Gutt J, Piepenburg D, Voß J. Asteroids, ophiuroids and holothurians from the southeastern Weddell Sea (Southern Ocean). Zookeys 2014:1-15. [PMID: 25152677 PMCID: PMC4141163 DOI: 10.3897/zookeys.434.7622] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 04/01/2014] [Accepted: 06/20/2014] [Indexed: 11/12/2022] Open
Abstract
Until the early 1980s, the composition and distribution of the asteroid (starfish), ophiuroid (brittle star) and holothurian (sea cucumber) bottom fauna of the southeastern Weddell Sea was virtually unknown. This southernmost part of the Atlantic sector of the Southern Ocean is a typical high-latitude Antarctic region located in the circumpolar permanent pack-ice zone. It became accessible for large-scale scientific surveys only through the availability of modern ice-breaking research vessels, such as the German RV “Polarstern”. Here, we describe a dataset of the faunal composition and abundance of starfish, brittle star and sea cucumber assemblages in this area, based on collections from trawl catches carried out during three “Polarstern” cruises in 1983, 1984 and 1985. The set comprises a total of 4,509 records of abundances of 35 asteroid species (with a total of 2,089 specimens) and 38 ophiuroid species (with a total of 18,484 specimens) from 34 stations, as well as of 66 holothurian species (with a total of 20,918 specimens) from 59 stations including zero-abundances (absences). A synthesizing zoogeographical community analysis confirms the presence of three distinct assemblages of asteroids, ophiuroids, and holothurians with highest species richness on the eastern shelf. Overall, starfishes, brittle stars and sea cucumbers were present at all sites investigated in the study area but composition and abundance of asterozoan (asteroids and ophiuroids together) and holothurian fauna varied considerably. A synthesizing zoogeographical community analysis confirms the presence of three distinct assemblages of asteroids, ophiuroids, and holothurians with highest species richness on the eastern shelf. In the case of asterozoans, water depth and latitude seemed to be the most important drivers of assemblage distribution and composition. One of the holothurian assemblages was part of the rich macrozoobenthic community dominated by a diverse and abundant epifauna, mainly sponges and gorgonians. Another one was mainly composed of vagrant deposit-feeding species inhabiting a predominantly non-colonised substratum. In addition, a mixed holothurian assemblage was identified.
Collapse
Affiliation(s)
- Julian Gutt
- Alfred Wegener Institute Hemholtz, Centre for Polar and Marine Research, Columbusstraße, 27515, Bremerhaven, Germany
| | - Dieter Piepenburg
- Alfred Wegener Institute Hemholtz, Centre for Polar and Marine Research, Columbusstraße, 27515, Bremerhaven, Germany
| | - Joachim Voß
- Landesamt für Landwirtschaft, Umwelt und ländliche Räume, Hamburger Chaussee 25, 24220, Flintbek, Germany
| |
Collapse
|
40
|
Carrillo-Rubio E, Kéry M, Morreale SJ, Sullivan PJ, Gardner B, Cooch EG, Lassoie JP. Use of multispecies occupancy models to evaluate the response of bird communities to forest degradation associated with logging. Conserv Biol 2014; 28:1034-1044. [PMID: 24628427 DOI: 10.1111/cobi.12261] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 03/21/2013] [Accepted: 11/14/2013] [Indexed: 06/03/2023]
Abstract
Forest degradation is arguably the greatest threat to biodiversity, ecosystem services, and rural livelihoods. Therefore, increasing understanding of how organisms respond to degradation is essential for management and conservation planning. We were motivated by the need for rapid and practical analytical tools to assess the influence of management and degradation on biodiversity and system state in areas subject to rapid environmental change. We compared bird community composition and size in managed (ejido, i.e., communally owned lands) and unmanaged (national park) forests in the Sierra Tarahumara region, Mexico, using multispecies occupancy models and data from a 2-year breeding bird survey. Unmanaged sites had on average higher species occupancy and richness than managed sites. Most species were present in low numbers as indicated by lower values of detection and occupancy associated with logging-induced degradation. Less than 10% of species had occupancy probabilities >0.5, and degradation had no positive effects on occupancy. The estimated metacommunity size of 125 exceeded previous estimates for the region, and sites with mature trees and uneven-aged forest stand characteristics contained the highest species richness. Higher estimation uncertainty and decreases in richness and occupancy for all species, including habitat generalists, were associated with degraded young, even-aged stands. Our findings show that multispecies occupancy methods provide tractable measures of biodiversity and system state and valuable decision support for landholders and managers. These techniques can be used to rapidly address gaps in biodiversity information, threats to biodiversity, and vulnerabilities of species of interest on a landscape level, even in degraded or fast-changing environments. Moreover, such tools may be particularly relevant in the assessment of species richness and distribution in a wide array of habitats.
Collapse
|
41
|
Waud M, Busschaert P, Ruyters S, Jacquemyn H, Lievens B. Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing. Mol Ecol Resour 2014; 14:679-99. [PMID: 24460947 DOI: 10.1111/1755-0998.12229] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 01/24/2023]
Abstract
Although the number of studies investigating mycorrhizal associations in orchids has increased in recent years, the fungal communities associating with orchids and how they differ between species and sites remain unclear. Recent research has indicated that individual orchid plants may associate with several fungi concurrently, implying that to study mycorrhizal associations in orchids the fungal community should be assessed, rather than the presence of individual dominant fungal species or strains. High-throughput sequencing methods, such as 454 pyrosequencing, are increasingly used as the primary tool for such analyses. However, many studies combine universal primers from previous phylogenetic or ecological studies to generate amplicons suitable for 454 pyrosequencing without first critically evaluating their performance, potentially resulting in biased fungal community descriptions. Here, following in silico primer analysis we evaluated the performance of different combinations of existing PCR primers to characterize orchid mycorrhizal communities using 454 pyrosequencing by analysis of both an artificially assembled community of mycorrhizal fungi isolated from diverse orchid species and root samples from three different orchid species (Anacamptis morio, Ophrys tenthredinifera and Serapias lingua). Our results indicate that primer pairs ITS3/ITS4OF and ITS86F/ITS4, targeting the internal transcribed spacer-2 (ITS-2) region, outperformed other tested primer pairs in terms of number of reads, number of operational taxonomic units recovered from the artificial community and number of different orchid mycorrhizal associating families detected in the orchid samples. Additionally, we show the complementary specificity of both primer pairs, making them highly suitable for tandem use when studying the diversity of orchid mycorrhizal communities.
Collapse
Affiliation(s)
- Michael Waud
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium; Division of Plant Ecology and Systematics, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001, Heverlee, Belgium
| | | | | | | | | |
Collapse
|
42
|
Wen A, Srinivasan U, Goldberg D, Owen J, Marrs CF, Misra D, Wing DA, Ponnaluri S, Miles-Jay A, Bucholz B, Abbas K, Foxman B. Selected vaginal bacteria and risk of preterm birth: an ecological perspective. J Infect Dis 2013; 209:1087-94. [PMID: 24273044 DOI: 10.1093/infdis/jit632] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We examined the community ecology of vaginal microbial samples taken from pregnant women with previous preterm birth experience to investigate whether targeted pathogenic and commensal bacteria are related to risk of preterm birth in the current pregnancy. We found a significant correlation between the community structure of selected bacteria and birth outcome, but the correlation differed among self-reported racial/ethnic groups. Using a community ordination analysis, we observed infrequent co-occurrence of Mycoplasma and bacteria vaginosis associated bacteria 3 (BVAB3) among black and Hispanic participants. In addition, we found that the vaginal bacteria responded differently in different racial/ethnic groups to modifications of maternal behavioral (ie, douching and smoking) and biological traits (ie, body mass index [BMI]). Even after accounting for these maternal behaviors and traits, the selected vaginal bacteria was significantly associated with preterm birth among black and Hispanic participants. By contrast, white participants did not exhibit significant correlation between microbial community and birth outcome. Findings from this study affirm the necessity of considering women's race/ethnicity when evaluating the correlation between vaginal bacteria and preterm birth. The study also illustrates the importance of studying the vaginal microbiota from an ecological perspective, and demonstrates the power of ecological community analysis to improve understanding of infectious disease.
Collapse
Affiliation(s)
- Ai Wen
- Department of Epidemiology
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Tully BJ, Heidelberg JF. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Front Microbiol 2013; 4:161. [PMID: 23805131 PMCID: PMC3691505 DOI: 10.3389/fmicb.2013.00161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 03/23/2013] [Accepted: 05/31/2013] [Indexed: 11/16/2022] Open
Abstract
The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the α-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment.
Collapse
Affiliation(s)
- Benjamin J Tully
- Department of Biological Science, Marine and Environmental Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California Los Angeles, CA, USA
| | | |
Collapse
|
44
|
Jung JH, Kim S, Ryu S, Kim MS, Baek YS, Kim SJ, Choi JK, Park JK, Min GS. Development of single-nucleotide polymorphism-based phylum-specific PCR amplification technique: application to the community analysis using ciliates as a reference organism. Mol Cells 2012; 34:383-91. [PMID: 22965748 PMCID: PMC3887769 DOI: 10.1007/s10059-012-0169-0] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 12/13/2022] Open
Abstract
Despite recent advance in mass sequencing technologies such as pyrosequencing, assessment of culture-independent microbial eukaryote community structures using universal primers remains very difficult due to the tremendous richness and complexity of organisms in these communities. Use of a specific PCR marker targeting a particular group would provide enhanced sensitivity and more in-depth evaluation of microbial eukaryote communities compared to what can be achieved with universal primers. We discovered that many phylum- or group-specific single-nucleotide polymorphisms (SNPs) exist in small subunit ribosomal RNA (SSU rRNA) genes from diverse eukaryote groups. By applying this discovery to a known simple allele-discriminating (SAP) PCR method, we developed a technique that enables the identification of organisms belonging to a specific higher taxonomic group (or phylum) among diverse types of eukaryotes. We performed an assay using two complementary methods, pyrosequencing and clone library screening. In doing this, specificities for the group (ciliates) targeted in this study in bulked environmental samples were 94.6% for the clone library and 99.2% for pyrosequencing, respectively. In particular, our novel technique showed high selectivity for rare species, a feature that may be more important than the ability to identify quantitatively predominant species in community structure analyses. Additionally, our data revealed that a target-specific library (or ciliate-specific one for the present study) can better explain the ecological features of a sampling locality than a universal library.
Collapse
Affiliation(s)
- Jae-Ho Jung
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
| | - Sanghee Kim
- Korea Polar Research Institute (KORDI), Songdo Techno Park, Incheon 406-840,
Korea
| | - Seongho Ryu
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065,
USA
| | - Min-Seok Kim
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
| | - Ye-Seul Baek
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
| | - Se-Joo Kim
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
- Present address: Deep-sea and Seabed Resources Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
| | - Joong- Ki Choi
- Department of Oceanography, Inha University, Incheon 402-751,
Korea
| | - Joong-Ki Park
- Department of Parasitology and Graduate Program in Cell Biology and Genetics, College of Medicine, Chungbuk National University, Cheongju 361-763,
Korea
| | - Gi-Sik Min
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
| |
Collapse
|