Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Conservation Biology and Biodiversity".

Deadline for manuscript submissions: closed (15 March 2023) | Viewed by 42116

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Guest Editor
Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
Interests: biogeochemical element cycling; protist biodiversity; agricultural plant–soil systems; sustainable agriculture; effects of silicon on plants; ecosystem functioning
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Department of Environment, University of the Aegean, 81132 Mytilene, Greece
Interests: biodiversity and ecosystem processes; functional plant ecology; community ecology; biodiversity conservation; conservation policy
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200333, China
Interests: biodiversity; conservation biology; evolutionary biology; population genetics; biotechnology; transgenic biosafety; agricultural botany

Special Issue Information

Dear Colleagues,

Numerous studies have proven that biodiversity and ecosystem functioning (BEF) are closely linked. In this context, the interactions between biodiversity and ecosystem functions such as productivity, nutrient cycling, decomposition, and pollination have been in the focus of research. Based on this, we now know that biodiversity usually promotes biomass production and pollination success, for example. However, regarding other BEF relationships, the drawing of general conclusions is hampered by the fact that different studies often show inconsistent results. Thus, for a better understanding of BEF relationships, detailed research on the underlying mechanisms is urgently needed. This knowledge is crucial to harmonize research findings and to craft policies for the conservation of biodiversity, which is severely threatened by global warming and other anthropogenic environmental changes.

We are inviting research articles and reviews dealing with all aspects of BEF relationships in terrestrial and aquatic communities. Papers on theoretical approaches, field and laboratory experiments as well as BEF studies in non-manipulated ecosystems are welcome. The aim of this Special Issue is to substantially deepen our understanding of BEF interactions and how to conserve biodiversity in a changing world.

Dr. Daniel Puppe
Prof. Dr. Panayiotis Dimitrakopoulos
Prof. Dr. Baorong Lu
Guest Editors

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Keywords

  • abiotic conditions
  • agroecosystem
  • biodiversity loss
  • biogeochemical element (e.g., carbon, nitrogen, silicon) cycling
  • carbon sequestration
  • community composition
  • decomposition
  • environmental heterogeneity
  • evolution
  • facilitation
  • functional diversity
  • functional traits
  • genetic diversity
  • global change
  • herbivore damage
  • local species pool
  • pathogens
  • pollination
  • primary productivity
  • realised diversity
  • resilience
  • resource partitioning
  • selection effect
  • species extinction
  • species richness

Published Papers (16 papers)

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Editorial

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3 pages, 210 KiB  
Editorial
Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities
by Daniel Puppe, Panayiotis G. Dimitrakopoulos and Baorong Lu
Biology 2023, 12(6), 835; https://doi.org/10.3390/biology12060835 - 9 Jun 2023
Viewed by 1339
Abstract
Numerous studies have proved that biodiversity and ecosystem functioning (BEF) are closely linked [...] Full article

Research

Jump to: Editorial, Review

21 pages, 3770 KiB  
Article
Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems
by Mohammad Sadegh Gheibzadeh, Colleen Varaidzo Manyumwa, Özlem Tastan Bishop, Hossein Shahbani Zahiri, Seppo Parkkila and Reza Zolfaghari Emameh
Biology 2023, 12(6), 770; https://doi.org/10.3390/biology12060770 - 25 May 2023
Cited by 1 | Viewed by 2065
Abstract
Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine [...] Read more.
Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean. Full article
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19 pages, 3403 KiB  
Article
Crop–Weed Introgression Plays Critical Roles in Genetic Differentiation and Diversity of Weedy Rice: A Case Study of Human-Influenced Weed Evolution
by Xing-Xing Cai, Zhi Wang, Ye Yuan, Li-Hao Pang, Ying Wang and Bao-Rong Lu
Biology 2023, 12(5), 744; https://doi.org/10.3390/biology12050744 - 19 May 2023
Cited by 3 | Viewed by 1220
Abstract
As an important driving force, introgression plays an essential role in shaping the evolution of plant species. However, knowledge concerning how introgression affects plant evolution in agroecosystems with strong human influences is still limited. To generate such knowledge, we used InDel (insertion/deletion) molecular [...] Read more.
As an important driving force, introgression plays an essential role in shaping the evolution of plant species. However, knowledge concerning how introgression affects plant evolution in agroecosystems with strong human influences is still limited. To generate such knowledge, we used InDel (insertion/deletion) molecular fingerprints to determine the level of introgression from japonica rice cultivars into the indica type of weedy rice. We also analyzed the impact of crop-to-weed introgression on the genetic differentiation and diversity of weedy rice, using InDel (insertion/deletion) and SSR (simple sequence repeat) molecular fingerprints. Results based on the STRUCTURE analysis indicated an evident admixture of some weedy rice samples with indica and japonica components, suggesting different levels of introgression from japonica rice cultivars to the indica type of weedy rice. The principal coordinate analyses indicated indicajaponica genetic differentiation among weedy rice samples, which was positively correlated with the introgression of japonica-specific alleles from the rice cultivars. In addition, increased crop-to-weed introgression formed a parabola pattern of dynamic genetic diversity in weedy rice. Our findings based on this case study provide evidence that human activities, such as the frequent change in crop varieties, can strongly influence weed evolution by altering genetic differentiation and genetic diversity through crop–weed introgression in agroecosystems. Full article
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23 pages, 7437 KiB  
Article
Adaptability of Wild-Growing Tulips of Greece: Uncovering Relationships between Soil Properties, Rhizosphere Fungal Morphotypes and Nutrient Content Profiles
by Fotis Bilias, Anastasia-Garyfallia Karagianni, Ioannis Ipsilantis, Ioulietta Samartza, Nikos Krigas, Georgios Tsoktouridis and Theodora Matsi
Biology 2023, 12(4), 605; https://doi.org/10.3390/biology12040605 - 16 Apr 2023
Cited by 4 | Viewed by 2279
Abstract
Wild-growing Greek tulips are protected plants but almost nothing is known about their natural nutrient status and rhizosphere fungal morphotypes in the wild, thus no insight is currently available into their growth and adaptation to their natural environment or artificial settings. To this [...] Read more.
Wild-growing Greek tulips are protected plants but almost nothing is known about their natural nutrient status and rhizosphere fungal morphotypes in the wild, thus no insight is currently available into their growth and adaptation to their natural environment or artificial settings. To this end, several botanical expeditions were conducted with a special collection permit, and 34 tulip and soil samples were collected, representing 13 species from two phytogeographical regions of Greece (North Aegean Islands, Crete Island) and seven regions of mainland Greece. The tulips’ content in essential macro- and micro-nutrients, respective physicochemical soil properties, and rhizosphere fungal morphotypes were assessed across samples, and all parameters were subjected to appropriate statistical analysis to determine their interrelationships. The results showed that soil variables played a significant role in shaping tulips’ nutrient content, explaining up to 67% of the detected variability as in the case of phosphorus (P) in the above-ground plant tissue. In addition, significant correlations were observed (with an r value of up to 0.65, p < 0.001) between essential nutrients in the tulips, such as calcium (Ca) and boron (B). The principal component analysis (PCA) revealed that between the three spatial units examined, the total variability of tulips’ nutrient content produced a clear distinction among sampled species, while the first two PCA axes managed to explain 44.3% of it. This was further confirmed by the analysis of variance (ANOVA) results which showed corresponding significant differences (at p < 0.05) in both the tulips’ nutrient content and the studied soil properties as well (mean values of N, P, and K in the North Aegean Islands tulips’ nutrient content, up to 53%, 119%, and 54% higher compared to those of the Crete Island, respectively). Our study sheds light on Greek tulips’ adaptability and resilience in their original habitats, facilitating at the same time the undertaken efforts regarding their conservation and potential domestication in artificial settings. Full article
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22 pages, 5933 KiB  
Article
Phenotypic Plasticity Strategy of Aeluropus lagopoides Grass in Response to Heterogenous Saline Habitats
by Abdulaziz M. Assaeed, Basharat A. Dar, Abdullah A. Al-Doss, Saud L. Al-Rowaily, Jahangir A. Malik and Ahmed M. Abd-ElGawad
Biology 2023, 12(4), 553; https://doi.org/10.3390/biology12040553 - 5 Apr 2023
Cited by 3 | Viewed by 1642
Abstract
Understanding the response variation of morphological parameters and biomass allocation of plants in heterogeneous saline environments is helpful in evaluating the internal correlation between plant phenotypic plasticity mechanism and biomass allocation. The plasticity of plants alters the interaction among individuals and their environment [...] Read more.
Understanding the response variation of morphological parameters and biomass allocation of plants in heterogeneous saline environments is helpful in evaluating the internal correlation between plant phenotypic plasticity mechanism and biomass allocation. The plasticity of plants alters the interaction among individuals and their environment and consequently affects the population dynamics and aspects of community and ecosystem functioning. The current study aimed to assess the plasticity of Aeluropus lagopoides traits with variation in saline habitats. Understanding the habitat stress tolerance strategy of A. lagopoides is of great significance since it is one of the highly palatable forage grass in the summer period. Five different saline flat regions (coastal and inland) within Saudi Arabia were targeted, and the soil, as well as the morphological and physiological traits of A. lagopoides, were assessed. Comprehensive correlation analyses were performed to correlate the traits with soil, region, or among each other. The soil analysis revealed significant variation among the five studied regions for all measured parameters, as well as among the soil layers showing the highest values in the upper layer and decreased with the depth. Significant differences were determined for all tested parameters of the morphological and reproductive traits as well as for the biomass allocation of A. lagopoides, except for the leaf thickness. In the highly saline region, Qaseem, A. lagopoides showed stunted aerial growth, high root/shoot ratio, improved root development, and high biomass allocation. In contrast, the populations growing in the low saline region (Jizan) showed the opposite trend. Under the more stressful condition, like in Qaseem and Salwa, A. lagopoides produce low spikes in biomass and seeds per plant, compared to the lowest saline habitats, such as Jouf. There was no significant difference in physiological parameters except stomatal conductance (gs), which is highest in the Jizan region. In conclusion, the population of A. lagopoides is tolerant of harsh environments through phenotypic plasticity. This could be a candidate species to rehabilitate the saline habitats, considering saline agriculture and saline soil remediation. Full article
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22 pages, 4822 KiB  
Article
Effect of Rice Straw and Stubble Burning on Soil Physicochemical Properties and Bacterial Communities in Central Thailand
by Noppol Arunrat, Sukanya Sereenonchai, Chakriya Sansupa, Praeploy Kongsurakan and Ryusuke Hatano
Biology 2023, 12(4), 501; https://doi.org/10.3390/biology12040501 - 26 Mar 2023
Cited by 13 | Viewed by 4373
Abstract
Rice straw and stubble burning is widely practiced to clear fields for new crops. However, questions remain about the effects of fire on soil bacterial communities and soil properties in paddy fields. Here, five adjacent farmed fields were investigated in central Thailand to [...] Read more.
Rice straw and stubble burning is widely practiced to clear fields for new crops. However, questions remain about the effects of fire on soil bacterial communities and soil properties in paddy fields. Here, five adjacent farmed fields were investigated in central Thailand to assess changes in soil bacterial communities and soil properties after burning. Samples of soil prior to burning, immediately after burning, and 1 year after burning were obtained from depths of 0 to 5 cm. The results showed that the pH, electrical conductivity, NH4-N, total nitrogen, and soil nutrients (available P, K, Ca, and Mg) significantly increased immediately after burning due to an increased ash content in the soil, whereas NO3-N decreased significantly. However, these values returned to the initial values. Chloroflexi were the dominant bacteria, followed by Actinobacteria and Proteobacteria. At 1 year after burning, Chloroflexi abundance decreased remarkably, whereas Actinobacteria, Proteobacteria, Verrucomicrobia, and Gemmatimonadetes abundances significantly increased. Bacillus, HSB OF53-F07, Conexibacter, and Acidothermus abundances increased immediately after burning, but were lower 1 year after burning. These bacteria may be highly resistant to heat, but grow slowly. Anaeromyxobacter and Candidatus Udaeobacter dominated 1 year after burning, most likely because of their rapid growth and the fact that they occupy areas with increased soil nutrient levels after fires. Amidase, cellulase, and chitinase levels increased with increased organic matter levels, whereas β-glucosidase, chitinase, and urease levels positively correlated with the soil total nitrogen level. Although clay and soil moisture strongly correlated with the soil bacterial community’s composition, negative correlations were found for β-glucosidase, chitinase, and urease. In this study, rice straw and standing stubble were burnt under high soil moisture and within a very short time, suggesting that the fire was not severe enough to raise the soil temperature and change the soil microbial community immediately after burning. However, changes in soil properties due to ash significantly increased the diversity indices, which was noticeable 1 year after burning. Full article
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14 pages, 3241 KiB  
Article
Giant Panda Microhabitat Study in the Daxiangling Niba Mountain Corridor
by Wei Jia, Shasha Yan, Qingqing He, Ping Li, Mingxia Fu and Jiang Zhou
Biology 2023, 12(2), 165; https://doi.org/10.3390/biology12020165 - 20 Jan 2023
Cited by 5 | Viewed by 2086
Abstract
Habitat reduction and increased fragmentation are urgent issues for the survival and recovery of the giant panda (Ailuropoda melanoleuca). However, changes in the distribution and microhabitat selection of giant panda habitats in different seasons in the same region have rarely been [...] Read more.
Habitat reduction and increased fragmentation are urgent issues for the survival and recovery of the giant panda (Ailuropoda melanoleuca). However, changes in the distribution and microhabitat selection of giant panda habitats in different seasons in the same region have rarely been assessed. To further understand giant panda habitat requirements, this study analyzed the giant panda habitat selection characteristics and differences using the sample data of the giant panda occurrence sites collected during 2020–2022. The results showed that the giant panda in both seasons selected medium altitudes (2000–2400 m), southeastern slopes, slopes less than 15°, taller tree layers (8–15 m) with a larger diameter at breast height (17–25 cm) and medium density (25–55%), shorter shrub layers (<4 m) with sparse density (<30%), and taller bamboo (>2 m) with high density (>35%). The giant panda microhabitat survey in the Niba Mountain corridor clarified the characteristics of suitable habitat selection for the giant panda in the corridor. The findings of the study can provide scientific references for the development of practical habitat conservation and management measures for giant pandas in the study area. Full article
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17 pages, 5219 KiB  
Article
Geology Can Drive the Diversity–Ecosystem Functioning Relationship in River Benthic Diatoms by Selecting for Species Functional Traits
by Evangelia Smeti, George Tsirtsis and Nikolaos Theodor Skoulikidis
Biology 2023, 12(1), 81; https://doi.org/10.3390/biology12010081 - 4 Jan 2023
Cited by 4 | Viewed by 2116
Abstract
The biodiversity–ecosystem functioning (BEF) relationship has been studied extensively for the past 30 years, mainly in terrestrial plant ecosystems using experimental approaches. Field studies in aquatic systems are scarce, and considering primary producers, they mainly focus on phytoplankton assemblages, whereas benthic diatoms in [...] Read more.
The biodiversity–ecosystem functioning (BEF) relationship has been studied extensively for the past 30 years, mainly in terrestrial plant ecosystems using experimental approaches. Field studies in aquatic systems are scarce, and considering primary producers, they mainly focus on phytoplankton assemblages, whereas benthic diatoms in rivers are considerably understudied in this regard. We performed a field study across nine rivers in Greece, and we coupled the observed field results with model simulations. We tested the hypothesis that the diversity–biomass (as a surrogate of ecosystem functioning) relationship in benthic diatoms would be affected by abiotic factors and would be time-dependent due to the highly dynamic nature of rivers. Indeed, geology played an important role in the form of the BEF relationship that was positive in siliceous and absent in calcareous substrates. Geology was responsible for nutrient concentrations, which, in turn, were responsible for the dominance of specific functional traits. Furthermore, model simulations showed the time dependence of the BEF form, as less mature assemblages tend to present a positive BEF. This was the first large-scale field study on the BEF relationship of benthic diatom assemblages, offering useful insights into the function and diversity of these overlooked ecosystems and assemblages. Full article
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17 pages, 2954 KiB  
Article
Assessing the Impact of Village Development on the Habitat Quality of Yunnan Snub-Nosed Monkeys Using the INVEST Model
by Shuxian Zhu, Li Li, Gongsheng Wu, Jialan Liu, Timothy J. Slate, Hongyan Guo and Dayong Li
Biology 2022, 11(10), 1487; https://doi.org/10.3390/biology11101487 - 11 Oct 2022
Cited by 6 | Viewed by 1694
Abstract
The habitats of the already endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) are degrading as village economies develop in and around these habitat areas, increasing the depopulation and biodiversity risk of the monkey. The paper aims to show the areas of these [...] Read more.
The habitats of the already endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) are degrading as village economies develop in and around these habitat areas, increasing the depopulation and biodiversity risk of the monkey. The paper aims to show the areas of these monkeys’ high-quality habitats that are at highest risk of degradation by continued village development and hence be the focus of conservation efforts. Our analysis leveraged multiple tools, including primary component analysis, the InVEST Habitat-Quality model, and GIS spatial analysis. We enhanced our analysis by looking at habitat quality as it relates to the habitat suitability for the monkey specifically, instead of general habitat quality. We also focused on the impact of the smallest administrative scale in China—the village. These foci produced a clearer picture of the monkeys’ and villages’ situations, allowing for more targeted discussions on win–win solutions for both the monkeys and the village inhabitants. The results show that the northern habitat for the monkey is currently higher quality than the southern habitat, and correspondingly, the village development in the north is lower than in the south. Hence, we recommend conservation efforts be focused on the northern areas, though we also encourage the southern habitats to be protected from further degradation lest they degrade beyond the point of supporting any monkeys. We encourage developing a strategy that balances ecological protection and economic development in the northern region, a long-term plan for the southern region to reduce human disturbance, increase effective habitat restoration, and improve corridor design. Full article
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14 pages, 2782 KiB  
Article
Keystone Taxa and Predictive Functional Analysis of Sphagnum palustre Tank Microbiomes in Erxianyan Peatland, Central China
by Baiying Man, Xing Xiang, Junzhong Zhang, Gang Cheng, Chao Zhang, Yang Luo and Yangmin Qin
Biology 2022, 11(10), 1436; https://doi.org/10.3390/biology11101436 - 30 Sep 2022
Cited by 1 | Viewed by 1568
Abstract
Sphagnum is a fundamental ecosystem of engineers, including more than 300 species around the world. These species host diverse microbes, either endosymbiotic or ectosymbiotic, and are key to carbon sequestration in peatland ecosystems. However, the linkages between different types of Sphagnum and the [...] Read more.
Sphagnum is a fundamental ecosystem of engineers, including more than 300 species around the world. These species host diverse microbes, either endosymbiotic or ectosymbiotic, and are key to carbon sequestration in peatland ecosystems. However, the linkages between different types of Sphagnum and the diversity and ecological functions of Sphagnum-associated microbiomes are poorly known, and so are their joint responses to ecological functions. Here, we systematically investigated endophytes in Sphagnum palustre via next-generation sequencing (NGS) techniques in the Erxianyan peatland, central China. The total bacterial microbiome was classified into 38 phyla and 55 classes, 122 orders and 490 genera. The top 8 phyla of Proteobacteria (33.69%), Firmicutes (11.94%), Bacteroidetes (9.42%), Actinobacteria (6.53%), Planctomycetes (6.37%), Gemmatimonadetes (3.05%), Acidobacteria (5.59%) and Cyanobacteria (1.71%) occupied 78.31% of total OTUs. The core microbiome of S. palustre was mainly distributed mainly in 7 phyla, 9 classes, 15 orders, 22 families and 43 known genera. There were many differences in core microbiomes compared to those in the common higher plants. We further demonstrate that the abundant functional groups have a substantial potential for nitrogen fixation, carbon cycle, nitrate metabolism, sulfate respiration and chitinolysis. These results indicate that potential ecological function of Sphagnum palustre in peatlands is partially rooted in its microbiomes, and that incorporating into functional groups of Sphagnum-associated microbiomes can promote mechanistic understanding of Sphagnum ecology in subalpine peatlands. Full article
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17 pages, 3210 KiB  
Article
Soil Microbial Diversity and Community Composition in Rice–Fish Co-Culture and Rice Monoculture Farming System
by Noppol Arunrat, Chakriya Sansupa, Praeploy Kongsurakan, Sukanya Sereenonchai and Ryusuke Hatano
Biology 2022, 11(8), 1242; https://doi.org/10.3390/biology11081242 - 20 Aug 2022
Cited by 29 | Viewed by 3821
Abstract
Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity [...] Read more.
Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility. Full article
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20 pages, 3424 KiB  
Article
Plant Diversity and Fungal Richness Regulate the Changes in Soil Multifunctionality in a Semi-Arid Grassland
by Zhuo Li, Xiaowei Liu, Minghui Zhang and Fu Xing
Biology 2022, 11(6), 870; https://doi.org/10.3390/biology11060870 - 6 Jun 2022
Cited by 10 | Viewed by 2946
Abstract
Loss in plant diversity is expected to impact biodiversity and ecosystem functioning (BEF) in terrestrial ecosystems. Soil microbes play essential roles in regulating ecosystem functions. However, the important roles and differences in bacterial and fungal diversity and rare microbial taxa in driving soil [...] Read more.
Loss in plant diversity is expected to impact biodiversity and ecosystem functioning (BEF) in terrestrial ecosystems. Soil microbes play essential roles in regulating ecosystem functions. However, the important roles and differences in bacterial and fungal diversity and rare microbial taxa in driving soil multifunctionality based on plant diversity remain poorly understood in grassland ecosystems. Here, we carried out an experiment in six study sites with varied plant diversity levels to evaluate the relationships between soil bacterial and fungal diversity, rare taxa, and soil multifunctionality in a semi-arid grassland. We used Illumina HiSeq sequencing to determine soil bacterial and fungal diversity and evaluated soil functions associated with the nutrient cycle. We found that high diversity plant assemblages had a higher ratio of below-ground biomass to above-ground biomass, soil multifunctionality, and lower microbial carbon limitation than those with low diversity. Moreover, the fungal richness was negatively and significantly associated with microbial carbon limitations. The fungal richness was positively related to soil multifunctionality, but the bacterial richness was not. We also found that the relative abundance of saprotrophs was positively correlated with soil multifunctionality, and the relative abundance of pathogens was negatively correlated with soil multifunctionality. In addition, the rare fungal taxa played a disproportionate role in regulating soil multifunctionality. Structural equation modeling showed that the shift of plant biomass allocation patterns increased plant below-ground biomass in the highly diverse plant plots, which can alleviate soil microbial carbon limitations and enhance the fungal richness, thus promoting soil multifunctionality. Overall, these findings expand our comprehensive understanding of the critical role of soil fungal diversity and rare taxa in regulating soil multifunctionality under global plant diversity loss scenarios. Full article
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23 pages, 21398 KiB  
Article
Effects of Trace Metals and Municipal Wastewater on the Ephemeroptera, Plecoptera, and Trichoptera of a Stream Community
by Marek Let, Jan Černý, Petra Nováková, Filip Ložek and Martin Bláha
Biology 2022, 11(5), 648; https://doi.org/10.3390/biology11050648 - 24 Apr 2022
Cited by 4 | Viewed by 2087
Abstract
Abundances of EPT larvae sampled in a Central European locality affected by mining and smelting, as well as by the continual inflow of treated communal wastewaters (WWs), were recorded. High concentrations of trace metals in water (maximum 1200 µg·L–1 for zinc) and [...] Read more.
Abundances of EPT larvae sampled in a Central European locality affected by mining and smelting, as well as by the continual inflow of treated communal wastewaters (WWs), were recorded. High concentrations of trace metals in water (maximum 1200 µg·L–1 for zinc) and sediments (maximum 140,000 mg·kg–1 in dry weight for lead) were found at the most contaminated sites. The highest loads of pesticides, pharmaceuticals, and illegal drugs were found under the WW effluent. Other associated factors such as the physicochemical parameters of the water and alterations to microhabitats were also evaluated and taken into account. Although EPT richness was lower at affected sites, abundances did not fall. Stoneflies were dominant at unaffected sites, while caddisflies dominated at affected sites. Only baetid mayflies were detected at the sites contaminated by trace metals and WWs; ephemerellid, heptageniid, and leptophlebiid mayflies were absent from these sites. The site contaminated by trace metals was also inhabited by numerous limnephilid caddisflies, in which limb malformations were detected in up to 11.8% of all specimens of a single taxon. Downstream from the entrance of the WWs, the locality was dominated by hydropsychid caddisflies. The increasing prevalence of predator or passive filter-feeding strategies in these EPT communities was significantly related to increasing water conductivity and acute ecosystemic exposure to ‘poorly treated’ WWs. Full article
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15 pages, 2302 KiB  
Article
Nutrient Accumulation Pattern in Mixtures of Wheat and Faba Bean Is Strongly Influenced by Cultivar Choice and Co-Existing Weeds
by James Ajal and Martin Weih
Biology 2022, 11(5), 630; https://doi.org/10.3390/biology11050630 - 20 Apr 2022
Cited by 2 | Viewed by 2434
Abstract
Cereal–legume mixtures are often associated with higher yields than the components grown as sole crops, but the underlying mechanisms are unclear. The study aims to evaluate how different cultivars in a two-species wheat–faba bean mixture influence above- and below-ground nitrogen (N) accumulation in [...] Read more.
Cereal–legume mixtures are often associated with higher yields than the components grown as sole crops, but the underlying mechanisms are unclear. The study aims to evaluate how different cultivars in a two-species wheat–faba bean mixture influence above- and below-ground nitrogen (N) accumulation in the plant biomass, whether crop mixing affected the accumulation of other nutrients relative to the accumulation of N and phosphorus (P), and how the nutrient accumulation pattern in sole crops and mixtures is influenced by weed competition. Using a growth container experiment, we investigate nutrient accumulation patterns on specific wheat and faba bean cultivars grown as sole crops and mixtures, and with and without weed competition. We found that cereals in the mixture accumulated more N than in the sole crops, and the cultivar used influenced biomass accumulation in the legumes. Competition from weeds reduced the amount of plant N pools accumulated in the crop plant biomass. Based on stoichiometric scaling exponents, the plant neighbor affected the accumulation of other nutrients relative to the accumulation of N and P. These results are relevant for species and cultivar selection, all of which are important prerequisites for maximizing mixture performance. Full article
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Review

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24 pages, 8216 KiB  
Review
Towards an Understanding of Large-Scale Biodiversity Patterns on Land and in the Sea
by Grégory Beaugrand
Biology 2023, 12(3), 339; https://doi.org/10.3390/biology12030339 - 21 Feb 2023
Cited by 1 | Viewed by 2665
Abstract
This review presents a recent theory named ‘macroecological theory on the arrangement of life’ (METAL). This theory is based on the concept of the ecological niche and shows that the niche-environment (including climate) interaction is fundamental to explain many phenomena observed in nature [...] Read more.
This review presents a recent theory named ‘macroecological theory on the arrangement of life’ (METAL). This theory is based on the concept of the ecological niche and shows that the niche-environment (including climate) interaction is fundamental to explain many phenomena observed in nature from the individual to the community level (e.g., phenology, biogeographical shifts, and community arrangement and reorganisation, gradual or abrupt). The application of the theory in climate change biology as well as individual and species ecology has been presented elsewhere. In this review, I show how METAL explains why there are more species at low than high latitudes, why the peak of biodiversity is located at mid-latitudes in the oceanic domain and at the equator in the terrestrial domain, and finally why there are more terrestrial than marine species, despite the fact that biodiversity has emerged in the oceans. I postulate that the arrangement of planetary biodiversity is mathematically constrained, a constraint we previously called ‘the great chessboard of life’, which determines the maximum number of species that may colonise a given region or domain. This theory also makes it possible to reconstruct past biodiversity and understand how biodiversity could be reorganised in the context of anthropogenic climate change. Full article
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16 pages, 1194 KiB  
Review
Marine Autotroph-Herbivore Synergies: Unravelling the Roles of Macroalgae in Marine Ecosystem Dynamics
by Acga Cheng, Wai Yin Lim, Phaik-Eem Lim, Affendi Yang Amri, Sze-Wan Poong, Sze-Looi Song and Zul Ilham
Biology 2022, 11(8), 1209; https://doi.org/10.3390/biology11081209 - 12 Aug 2022
Cited by 2 | Viewed by 4965
Abstract
Species invasion is a leading threat to marine ecosystems worldwide, being deemed as one of the ultimate jeopardies for biodiversity along with climate change. Tackling the emerging biodiversity threat to maintain the ecological balance of the largest biome in the world has now [...] Read more.
Species invasion is a leading threat to marine ecosystems worldwide, being deemed as one of the ultimate jeopardies for biodiversity along with climate change. Tackling the emerging biodiversity threat to maintain the ecological balance of the largest biome in the world has now become a pivotal part of the Sustainable Development Goals (SDGs). Marine herbivores are often considered as biological agents that control the spread of invasive species, and their effectiveness depends largely on factors that influence their feeding preferences, including the specific attributes of their food–the autotrophs. While the marine autotroph-herbivore interactions have been substantially discussed globally, many studies have reported contradictory findings on the effects of nutritional attributes and novelty of autotrophs on herbivore feeding behaviour. In view of the scattered literature on the mechanistic basis of autotroph-herbivore interactions, we generate a comprehensive review to furnish insights into critical knowledge gaps about the synergies based largely on the characteristics of macroalgae; an important group of photosynthetic organisms in the marine biome that interact strongly with generalist herbivores. We also discuss the key defence strategies of these macroalgae against the herbivores, highlighting their unique attributes and plausible roles in keeping the marine ecosystems intact. Overall, the feeding behaviour of herbivores can be affected by the nutritional attributes, morphology, and novelty of the autotrophs. We recommend that future research should carefully consider different factors that can potentially affect the dynamics of the marine autotroph-herbivore interactions to resolve the inconsistent results of specific attributes and novelty of the organisms involved. Full article
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