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Special Issue "Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities"

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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 12773

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Special Issue Editors

Dr. Daniel Puppe

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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

Prof. Dr. Panayiotis Dimitrakopoulos

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Guest Editor

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

Prof. Dr. Baorong Lu

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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 (11 papers)

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Research

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Open AccessArticle

Effect of Rice Straw and Stubble Burning on Soil Physicochemical Properties and Bacterial Communities in Central Thailand

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Biology 2023, 12(4), 501; https://doi.org/10.3390/biology12040501 - 26 Mar 2023

Viewed by 313

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessArticle

Giant Panda Microhabitat Study in the Daxiangling Niba Mountain Corridor

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Biology 2023, 12(2), 165; https://doi.org/10.3390/biology12020165 - 20 Jan 2023

Viewed by 845

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessArticle

Geology Can Drive the Diversity–Ecosystem Functioning Relationship in River Benthic Diatoms by Selecting for Species Functional Traits

Evangelia Smeti

George Tsirtsis

and

Nikolaos Theodor Skoulikidis

Biology 2023, 12(1), 81; https://doi.org/10.3390/biology12010081 - 04 Jan 2023

Viewed by 1112

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessArticle

Assessing the Impact of Village Development on the Habitat Quality of Yunnan Snub-Nosed Monkeys Using the INVEST Model

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Biology 2022, 11(10), 1487; https://doi.org/10.3390/biology11101487 - 11 Oct 2022

Cited by 1 | Viewed by 739

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessArticle

Keystone Taxa and Predictive Functional Analysis of Sphagnum palustre Tank Microbiomes in Erxianyan Peatland, Central China

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Biology 2022, 11(10), 1436; https://doi.org/10.3390/biology11101436 - 30 Sep 2022

Viewed by 655

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessArticle

Soil Microbial Diversity and Community Composition in Rice–Fish Co-Culture and Rice Monoculture Farming System

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Biology 2022, 11(8), 1242; https://doi.org/10.3390/biology11081242 - 20 Aug 2022

Cited by 7 | Viewed by 1516

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessArticle

Plant Diversity and Fungal Richness Regulate the Changes in Soil Multifunctionality in a Semi-Arid Grassland

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Biology 2022, 11(6), 870; https://doi.org/10.3390/biology11060870 - 06 Jun 2022

Cited by 2 | Viewed by 1357

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessArticle

Effects of Trace Metals and Municipal Wastewater on the Ephemeroptera, Plecoptera, and Trichoptera of a Stream Community

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Biology 2022, 11(5), 648; https://doi.org/10.3390/biology11050648 - 24 Apr 2022

Cited by 2 | Viewed by 1116

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessArticle

Nutrient Accumulation Pattern in Mixtures of Wheat and Faba Bean Is Strongly Influenced by Cultivar Choice and Co-Existing Weeds

James Ajal

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Martin Weih

Biology 2022, 11(5), 630; https://doi.org/10.3390/biology11050630 - 20 Apr 2022

Viewed by 1279

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Review

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Open AccessReview

Towards an Understanding of Large-Scale Biodiversity Patterns on Land and in the Sea

Grégory Beaugrand

Biology 2023, 12(3), 339; https://doi.org/10.3390/biology12030339 - 21 Feb 2023

Viewed by 606

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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Open AccessReview

Marine Autotroph-Herbivore Synergies: Unravelling the Roles of Macroalgae in Marine Ecosystem Dynamics

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Biology 2022, 11(8), 1209; https://doi.org/10.3390/biology11081209 - 12 Aug 2022

Viewed by 1490

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 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

(This article belongs to the Special Issue Biodiversity and Ecosystem Functioning in Naturally and Experimentally Assembled Communities)

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