Ecologies

Editorial

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2 pages, 202 KiB

Open AccessEditorial

Feature Papers in Ecology 2022 and the Remarkable Journal’s Advancements

by José Ramón Arévalo

Ecologies 2023, 4(3), 461-462; https://doi.org/10.3390/ecologies4030029 - 4 Jul 2023

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Abstract

The journal Ecologies experienced continuous growth throughout the year 2022 [...] Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

Research

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14 pages, 1575 KiB

Open AccessArticle

Influence of Agricultural Expansion and Human Disturbance on the Encounter Rates of Nocturnal Mammals in Tropical Hill Forests in Bangladesh

by Hassan Al-Razi, Marco Campera, Sabit Hasan, Marjan Maria, Vincent Nijman and K. Anne-Isola Nekaris

Ecologies 2023, 4(1), 195-208; https://doi.org/10.3390/ecologies4010014 - 22 Mar 2023

Cited by 2 | Viewed by 2694

Abstract

Agricultural expansion has had a detrimental effect on tropical forests and the animal communities that depend on them. Agroforestry systems, however, with their more complex tree and plant communities, have been shown to be important habitats for a range of globally threatened species, [...] Read more.

Agricultural expansion has had a detrimental effect on tropical forests and the animal communities that depend on them. Agroforestry systems, however, with their more complex tree and plant communities, have been shown to be important habitats for a range of globally threatened species, including nocturnal animals. Here, we present novel data on the encounter rates of seven species of nocturnal mammals in relation to agroforestry systems within four national parks and associated plantations in Bangladesh to examine if encounter rates were influenced by the human population density, presence of plantations, and human access as represented by a Human Influence Index of anthropogenic disturbance. We walked 70.3 km of transects with only semi-natural forest, 26.9 km of transects with semi-natural forest and gardens, and 21.7 km of transects with semi-natural forest and monocultures over 55 nights from 2017–2019. Of the seven species of nocturnal mammals we detected, all were present in Satachari National Park, whereas six occurred in Lawachara National Park, Rajkandi Forest Range, and Rema-Kalenga Wildlife Sanctuary. Within these national parks, three species (Bengal slow loris, large Indian civet, particolored flying squirrel) were more frequently recorded in areas with human disturbance, especially agroforestry plantations. With declining forest cover in Bangladesh, we highlight here the potential of agroforestry systems as emerging important habitats for these species. We encourage long-term studies of these lesser-studied taxa to understand fully the capacity of agroforestry systems in order to support their long-term conservation. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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19 pages, 3244 KiB

Open AccessArticle

Culturable Diversity of Lichen-Associated Yeasts through Enrichment Strategies

by Daniel B. Raudabaugh and M. Catherine Aime

Ecologies 2023, 4(1), 152-170; https://doi.org/10.3390/ecologies4010012 - 2 Mar 2023

Cited by 3 | Viewed by 3912

Abstract

Lichens are symbiotic partnerships between a filamentous fungus and a photosymbiotic “alga”. Studies show that lichens harbor endothallic fungi, but that some taxa have been difficult to isolate from the main filamentous thallus-forming fungus and other faster growing lichenicolous/endothallic fungi. Therefore, we aimed [...] Read more.

Lichens are symbiotic partnerships between a filamentous fungus and a photosymbiotic “alga”. Studies show that lichens harbor endothallic fungi, but that some taxa have been difficult to isolate from the main filamentous thallus-forming fungus and other faster growing lichenicolous/endothallic fungi. Therefore, we aimed to develop and evaluate liquid yeast-enrichment strategies to (1) isolate lichen-associated yeasts in pure culture, and (2) determine the taxonomic placement and breadth of the diversity of culturable yeasts. Eighty-two lichen samples were collected and washed with distilled water, and healthy thalli were ground up and added to seven different yeast-enrichment broths. Yeast colonies were isolated in pure culture and identified using molecular techniques. Initial isolates were identified using BLASTn analysis, and a taxonomic refinement was completed using PhyML analysis. In total, 215 isolates were obtained. The most prevalently isolated ascomycetous yeasts were within the Dothideomycetes (Aureobasidium, Plowrightia, and Dothiora), while the most frequently isolated basidiomycetous yeasts belonged to the genera Curvibasidium, Sporobolomyces, and Tremella. The generic placements could not be determined for 17 isolates, and in total 25 novel species were recovered. The results of this research indicate that (1) lichen-associated yeasts are diverse, (2) employing liquid enrichment strategies is effective for isolating many of these, and (3) lichen thalli represent a valuable untapped reservoir of diverse and novel yeast species. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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17 pages, 2835 KiB

Open AccessArticle

Investigation of Cowpea (Vigna unguiculata (L.) Walp.)–Insect Pollinator Interactions Aiming to Increase Cowpea Yield and Define New Breeding Tools

by Efstathia Lazaridi, María J. Suso, F. Javier Ortiz-Sánchez and Penelope J. Bebeli

Ecologies 2023, 4(1), 124-140; https://doi.org/10.3390/ecologies4010010 - 14 Feb 2023

Cited by 8 | Viewed by 4566

Abstract

Impact of pollination on the agri-food sector is of paramount importance. Pollinators contribute to the maintenance of ecosystems, the reproduction and survival of many plants, and their presence usually leads to increased yield and quality of agricultural products. Breeding and selecting for plant [...] Read more.

Impact of pollination on the agri-food sector is of paramount importance. Pollinators contribute to the maintenance of ecosystems, the reproduction and survival of many plants, and their presence usually leads to increased yield and quality of agricultural products. Breeding and selecting for plant traits for enhancing pollinator visits could therefore lead to more resilient farming systems. In stating the advantages of enhancing pollinators in agricultural systems, this study was designed aiming to assess six cowpea accessions for their flower traits and their effect on insect-pollinators. Pollinators species abundance and foraging activity was recorded and their impact on yield was investigated. Twenty-five of the twenty-seven flower traits studied differed statistically significantly among cowpea accessions. The main pollinators recorded belonged to the genus Xylocopa (Latreille, 1802). Seed and fresh pod yield was not affected by pollinators. The floral traits related to pollinators abundance and foraging activity were flower color, inflorescence position and the hours that the flowers per plant remained open during the day. However, they were not related linearly to pollinators abundance and foraging activity; therefore, they did not constitute safe traits for selection aiming to increase pollinators visitation. The findings suggested that other traits, such as pollen and nectar reward, probably perform a more important role in attracting pollinators compared to flower traits. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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18 pages, 7316 KiB

Open AccessArticle

Taxonomic Diversity of the Microbial Biofilms Collected along the Thermal Streams on Kunashir Island

by Alexandra Malygina, Alexander Balkin, Elena Polyakova, Sergey Stefanov, Alexey Potekhin and Natalia Gogoleva

Ecologies 2023, 4(1), 106-123; https://doi.org/10.3390/ecologies4010009 - 10 Feb 2023

Cited by 5 | Viewed by 2734

Abstract

Hot springs are known as highly adverse extreme environments where thermophilic and hyperthermophilic microorganisms can survive. We describe taxonomic diversity of several microbial biofilms collected along water temperature gradient in hot streams in the aquatic system of the Stolbovskie hot springs on Kunashir [...] Read more.

Hot springs are known as highly adverse extreme environments where thermophilic and hyperthermophilic microorganisms can survive. We describe taxonomic diversity of several microbial biofilms collected along water temperature gradient in hot streams in the aquatic system of the Stolbovskie hot springs on Kunashir Island, Kurils, Russia. The taxonomic composition of the studied microbial communities was assessed by the 16S rRNA gene metabarcoding for bacteria and archaea, and by the 18S rRNA gene metabarcoding for protists. Richness and diversity of bacteria in the geothermal microbial communities decreased with the increase of temperature, while for archaea, the tendency was the opposite. Ciliophora was the most represented taxon of protists. The biofilms of various kinds that we found in a very local area of the geothermal system were different from each other by taxonomic composition, and the level of their taxonomic diversity was significantly influenced by water temperature. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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14 pages, 2230 KiB

Open AccessArticle

Linking Rhizosphere Soil Aggregates with Belowground and Aboveground Plant Traits

by Md Imam ul Khabir, Daphne Topps, Jannatul Ferdous Jhumur, Anthony Adesemoye, Jasmine Brown, Antoine Newman, Boakai K. Robertson, Javed Iqbal and Muhammad Saleem

Ecologies 2023, 4(1), 74-87; https://doi.org/10.3390/ecologies4010007 - 8 Feb 2023

Cited by 1 | Viewed by 2180

Abstract

Rhizosphere soil ecosystems are represented by the diversity of different soil aggregate-size classes, such as large macroaggregates, small macroaggregates, mesoaggregates, and microaggregates. Though these aggregate-size classes represent distinct biological, chemical, and physical properties, little is known about their dynamics and relationships with belowground [...] Read more.

Rhizosphere soil ecosystems are represented by the diversity of different soil aggregate-size classes, such as large macroaggregates, small macroaggregates, mesoaggregates, and microaggregates. Though these aggregate-size classes represent distinct biological, chemical, and physical properties, little is known about their dynamics and relationships with belowground and aboveground plant traits. In this study, we examined the relationships of various soil aggregate-size classes and their organic carbon contents with many aboveground and belowground soybean plant traits. Our study revealed several novel and interesting relationships between soil structural properties and plant traits. Notably, small macroaggregates represented a major portion of the rhizosphere soil ecosystem of soybean plants while organic carbon contents decreased with decreasing size of soil aggregates. Only microaggregates showed a significant relationship with root architectural traits, such as length and surface area. Among all soil aggregate size classes, the abundance of small macroaggregates and the organic carbon contents of microaggregates were better correlated with plant traits. In general, organic carbon contents of different soil aggregate-size classes showed positive correlations with leaf trichome density (defense traits) and major macronutrients, such as root P, K, and S contents; while there were mostly negative correlations with some micronutrient (Ca, Mn, Zn, Cu, B, and Mg) contents of roots and shoots. However, the abundance of small macroaggregates mostly positively correlated with the mineral contents of plant roots and shoots. Collectively, the positive and negative correlations of organic carbon contents of different soil aggregate-size classes with trichomes (defense) and physiological traits (micro-mineral contents) suggest their significance in plant nutrition and defense. Though our results suggest the relationships of soil aggregate properties with aboveground and belowground traits, further research is needed to discern the role of soil structural traits in mediating plant growth, development, defense, and physiology. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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14 pages, 2041 KiB

Open AccessArticle

Wild Felid Diversity, Space Use and Activity Patterns in the Eastern Himalaya, India

by Tawqir Bashir, Tapajit Bhattacharya, Kamal Poudyal and Sambandam Sathyakumar

Ecologies 2023, 4(1), 41-54; https://doi.org/10.3390/ecologies4010005 - 25 Jan 2023

Cited by 2 | Viewed by 3080

Abstract

Species with similar resource requirements cannot coexist for long. To facilitate co-existence, carnivores adapt different strategies to partition the available resources in space and time. In high-altitude ecosystems with limited resources the operation becomes complex. We assessed species diversity and spatio-temporal resource partitioning [...] Read more.

Species with similar resource requirements cannot coexist for long. To facilitate co-existence, carnivores adapt different strategies to partition the available resources in space and time. In high-altitude ecosystems with limited resources the operation becomes complex. We assessed species diversity and spatio-temporal resource partitioning among felid species inhabiting the intricate habitats of Khangchendzonga Biosphere Reserve (KBR), Eastern Himalaya. We used systematic camera trap surveys along with abundance and overlap indices to generate information on their space use and activity patterns. We recorded six species of felids belonging to five genera, including four species of global conservation importance. The differential use of space by felids was observed with respect to the habitat types determined by sharp altitudinal gradients with varied levels of spatial and altitudinal overlap. Maximum overlap was observed among Asiatic golden cat Catopuma temminckii, jungle cat Felis chaus and clouded leopard Neofelis nebulosa. The felids had distinct activity profiles from one other, particularly between golden cat and leopard cat Prionailurus bengalensis. Pianka’s index also provided weak evidence for temporal overlap among species. The overall results indicate that habitat heterogeneity facilitates primary separation at the spatial scale, although species are also segregated temporally. Golden cat was the most adaptive felid in the area, depicting a peculiar pattern of spatio-temporal segregation with other species. We suspect either intense competition or dietary segregation among some species, and propose a further investigation of their diet and the activity patterns of their prey. The study presents an early template of carnivore community organization in resource-scarce high-altitude environments, thus, offering huge ecological and conservation significance. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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9 pages, 1114 KiB

Open AccessArticle

Ecological Half-Life of ¹³⁷Cs in Fungi

by Nataliia E. Zarubina, Vladislav Semak, Oleg S. Burdo and Liliia P. Ponomarenko

Ecologies 2023, 4(1), 11-19; https://doi.org/10.3390/ecologies4010002 - 21 Dec 2022

Cited by 2 | Viewed by 2116

Abstract

The ecological half-life of ¹³⁷Cs was calculated individually for four symbiotrophic fungi species (Boletus edulis, Imleria badia, Suillus luteus, Paxillus involutus) at 10 sampling sites in the Chornobyl exclusion zone and in the Kyiv region. It was [...] Read more.

The ecological half-life of ¹³⁷Cs was calculated individually for four symbiotrophic fungi species (Boletus edulis, Imleria badia, Suillus luteus, Paxillus involutus) at 10 sampling sites in the Chornobyl exclusion zone and in the Kyiv region. It was found that the maximum rate of excretion of 137Cs from the fungi organisms is characteristic for the territory with the maximum levels of soil contamination, i.e., for a zone near Chornobyl Nuclear Power Plant. In areas with low ¹³⁷Cs content, a slowing down of the excretion rate predominates. These results reveal different fungal response to the distinct concentration levels of ¹³⁷Cs in forest ecosystems. This observation further suggests that radiocaesium can be selectively accumulated by fungi and used in their life processes. Presence of this ¹³⁷Cs retention mechanism in fungi leads to a longer contamination of woody plants-symbionts. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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10 pages, 1071 KiB

Open AccessArticle

Pollinator Communities of Planted and Feral Pyrus calleryana

by Benjamin J. Dolan, Abby L. Kalkstein, Madeline Haase, Paige Chernisky, Alivia Niese, Ashlie N. Hicks and Dolly Miller

Ecologies 2023, 4(1), 1-10; https://doi.org/10.3390/ecologies4010001 - 21 Dec 2022

Cited by 1 | Viewed by 2970

Abstract

Pyrus calleryana was intentionally introduced to North America from east Asia in the early 1900s as rootstock for the edible pear tree, Pyrus communis. It was identified as an ideal decorative, agricultural, and horticultural tree because of its small stature, early spring flowering, [...] Read more.

Pyrus calleryana was intentionally introduced to North America from east Asia in the early 1900s as rootstock for the edible pear tree, Pyrus communis. It was identified as an ideal decorative, agricultural, and horticultural tree because of its small stature, early spring flowering, fire blight resistance and inoffensive fruits. P. calleryana escaped cultivation and is now considered an invasive species, typically found on roadsides, prairies, and fields. The aim of this study is to characterize pollinator community diversity from planted and feral trees, as well as diversity as it compares to expected communities derived from research-grade iNaturalist observations. Pollinators were collected by hand on planted and feral P. calleryana trees in April 2018–2022. A total of 14 taxa of insect pollinator were collected from P. calleryana flowers, with similar levels of diversity of pollinator taxa collected from planted and feral trees, and Apis mellifera and Andrena spp. the most common taxa observed. The sampled pollinator community did not differ from the expected pollinator communities generated using the iNaturalist data on either the planted or feral P. calleryana. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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9 pages, 2925 KiB

Open AccessArticle

Is the Tea Bag Index (TBI) Useful for Comparing Decomposition Rates among Soils?

by Taiki Mori

Ecologies 2022, 3(4), 521-529; https://doi.org/10.3390/ecologies3040038 - 15 Nov 2022

Cited by 8 | Viewed by 3363

Abstract

The Bag Index (TBI) is a novel approach using standardized materials (i.e., commercial tea bags) to evaluate organic matter decomposition by determining two indexes: the early stage decomposition constant k (k_TBI) and litter stabilization factor S (S_TBI). k_TBI is [...] Read more.

The Bag Index (TBI) is a novel approach using standardized materials (i.e., commercial tea bags) to evaluate organic matter decomposition by determining two indexes: the early stage decomposition constant k (k_TBI) and litter stabilization factor S (S_TBI). k_TBI is defined as the decomposition constant of an asymptote model describing the decomposition curve of rooibos tea, whereas S is the ratio of the stabilized to total hydrolysable fractions of green tea. However, it was recently revealed that both k_TBI and S_TBI deviate from the actual S and k values accurately determined by fitting an asymptote model to the time series mass of green and rooibos teas remaining (k_fitting and S_fitting, respectively). Nevertheless, k_TBI and S_TBI, which can be determined in a cost- and labor-effective manner, might indicate the relative values of k_fitting and S_fitting across different soils and be useful for comparative analyses. Therefore, this study investigated the positive correlations of k_TBI and S_TBI with k_fitting and S_fitting, respectively, in which case these indexes are useful for comparative analyses. However, the result showed that k_TBI was negatively correlated with k_fitting. This study underscores the importance of obtaining time-series data for accurately determining the decomposition constant of an asymptote model describing the decomposition curve of rooibos tea. S_TBI was positively correlated with S_fitting, implying that S_TBI can be used as an indicator of S. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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11 pages, 2203 KiB

Open AccessArticle

Susceptibility of Tidal Pool Fish Assemblages to Climate Change

by Tom R. Davis and Matt Nimbs

Ecologies 2022, 3(4), 510-520; https://doi.org/10.3390/ecologies3040037 - 4 Nov 2022

Cited by 1 | Viewed by 2676

Abstract

There is a need for improved understanding of how climate-change driven rises in sea level and increased ocean temperatures will affect fish assemblages in rocky shore tidal pools. Rising sea levels are predicted to alter habitat availability and increasing ocean temperatures will drive [...] Read more.

There is a need for improved understanding of how climate-change driven rises in sea level and increased ocean temperatures will affect fish assemblages in rocky shore tidal pools. Rising sea levels are predicted to alter habitat availability and increasing ocean temperatures will drive tropicalisation, both of which are likely to alter tidal pool fish assemblages. Consequently, we examined changes in fish assemblages in tidal pools at four sites in Coffs Harbour, Australia, using baited video sampling. Data were collected seasonally at each site, in pools at differing tidal elevations. We identified significant differences in tidal pool fish assemblages among elevations and found that assemblages exhibited cyclic seasonal patterns. Modelling identified that ocean temperature was the most powerful factor for explaining variations in assemblages, followed by pool area and pool elevation. Results highlight that distinct fish assemblages occur in tidal pools at different elevations and indicate that assemblages at higher elevations could be squeezed out by rising sea levels and by increased competition from tropical fish species. Future conservation assessments are needed to determine whether latitudinal and vertical range shifts for tidal pool fishes are possible, with facilitation of these range shifts needed to address displacement of tidal pool fishes by rising sea levels and ocean temperatures. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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21 pages, 2240 KiB

Open AccessArticle

Long-Term Changes in Abundance and Composition of Forest-Floor Small Mammal Communities in a Landscape with Cumulative Clearcutting

by Thomas P. Sullivan and Druscilla S. Sullivan

Ecologies 2022, 3(4), 446-466; https://doi.org/10.3390/ecologies3040032 - 2 Oct 2022

Cited by 2 | Viewed by 2359

Abstract

Responses of forest-floor small mammals to clearcutting are species-specific with generalists occupying a range of habitats, and specialists persisting on clearcuts for variable periods. We investigated the responses in abundance and species composition of small mammal communities to cumulative clearcutting of coniferous forests [...] Read more.

Responses of forest-floor small mammals to clearcutting are species-specific with generalists occupying a range of habitats, and specialists persisting on clearcuts for variable periods. We investigated the responses in abundance and species composition of small mammal communities to cumulative clearcutting of coniferous forests on a landscape that had four independent clearcutting events (Periods 1 to 4) over a 42-year interval from 1979 to 2020 in south-central British Columbia, Canada. We ask if the small mammal communities have changed significantly over these decades owing to removal of old-growth forest by clearcut harvesting. Hypotheses (H) predicted that the small mammal community would (H₁) increase in abundance, species richness, and diversity on new clearcuts owing to the availability of early seral post-harvest habitats from cumulative clearcutting; and (H₂) have higher mean abundance, species richness, and species diversity in clearcut than uncut forest sites, owing to availability of vegetative food and cover. A third hypothesis (H₃) predicted that abundance of (i) early seral vegetation (herbs and shrubs) and (ii) small mammal populations, will be greater in ungrazed clearcut sites than in those grazed by cattle (Bos taurus). Mean total numbers of small mammals on new clearcuts declined in Periods 3 and 4, and hence did not support the abundance part of H₁. Much of this decline was owing to low numbers of the long-tailed vole (Microtus longicaudus) and meadow vole (M. pennsylvanicus). Two generalist species: the deer mouse (Peromyscus maniculatus) and northwestern chipmunk (Neotamias amoenus), contributed to high mean species richness and diversity in Periods 2 and 3 before these metrics declined in Period 4, and hence partly supported H₁. The similarity in mean total numbers of small mammals in Periods 2 to 4 did not support the abundance prediction of H₂ that total numbers would be higher in clearcut than uncut forest sites. Higher mean species richness (Periods 2 and 3) and diversity (Period 3) measurements on clearcut than forest sites, particularly in the early post-harvest years, did support these parts of H₂. The vegetation part (i) of H₃ was not supported for herbaceous plants but it was for shrubs. The small mammal part (ii) of H₃ that populations would be higher in ungrazed than grazed clearcut sites was supported for abundance but not for species richness or diversity. The decline and near disappearance of both species of Microtus was possibly related to the reduction in plant community abundance and structure from grazing (at least for shrubs) and potentially from drought effects associated with climate change. Loss of microtines from these early seral ecosystems may have profound negative effects on various ecological functions and predator communities. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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13 pages, 2110 KiB

Open AccessArticle

Localized Placement of Breakwater Reefs Influences Oyster Populations and Their Resilience after Hurricane Harvey

by Marc H. Hanke, Haille Leija, Robert A. S. Laroche, Shailee Modi, Erin Culver-Miller, Rachel Sanchez and Neha Bobby

Ecologies 2022, 3(3), 422-434; https://doi.org/10.3390/ecologies3030030 - 18 Sep 2022

Cited by 2 | Viewed by 2400

Abstract

Populations of the eastern oyster (Crassostrea virginica) have been historically declining due to both natural and anthropogenic stressors. In response, oyster reefs have been created with many different approaches. This study utilized intertidal reefs constructed with oyster shells recycled from local [...] Read more.

Populations of the eastern oyster (Crassostrea virginica) have been historically declining due to both natural and anthropogenic stressors. In response, oyster reefs have been created with many different approaches. This study utilized intertidal reefs constructed with oyster shells recycled from local restaurants to provide oyster settlement substrate, reef-associated faunal habitat, and a barrier to prevent marsh erosion. The objective of this study was to determine how oyster population characteristics changed over four years (2016–2019) on five different reefs within Sweetwater Lake, Galveston Bay, Texas, with a secondary objective to examine how oyster populations responded after Hurricane Harvey. Over the study period, five different reefs were sampled each summer by removing five bags per reef to determine oyster abundance and size demography. For the three years of the study (2017–2019), we also quantified oyster spat recruitment to the reefs. Oyster abundance and size (shell height) varied interactively by year and reef number, whereas oyster recruitment was significantly lower following Hurricane Harvey and then returned to pre-storm levels. Our results further highlight the importance of reef placement for breakwater-style reefs, as it appears the hydrodynamics within Sweetwater Lake influenced both oyster abundance and size among individual reefs. While the created reefs receive limited larval influx due to the narrow opening between Sweetwater Lake and Galveston Bay proper, this limited connectivity seemed to prevent mass mortality from the freshwater influx from Hurricane Harvey. Therefore, projects creating oyster reefs should consider local and regional landscape factors for the long-term success of oyster populations and robustness to natural disasters. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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13 pages, 3478 KiB

Open AccessArticle

Dominant Species-Physiognomy-Ecological (DSPE) System for the Classification of Plant Ecological Communities from Remote Sensing Images

by Ram C. Sharma

Ecologies 2022, 3(3), 323-335; https://doi.org/10.3390/ecologies3030025 - 12 Aug 2022

Cited by 10 | Viewed by 2449

Abstract

This paper presents the Dominant Species-Physiognomy-Ecological (DSPE) classification system developed for large-scale differentiation of plant ecological communities from high-spatial resolution remote sensing images. In this system, the plant ecological communities are defined with the inference of dominant species, physiognomy, and shared ecological settings [...] Read more.

This paper presents the Dominant Species-Physiognomy-Ecological (DSPE) classification system developed for large-scale differentiation of plant ecological communities from high-spatial resolution remote sensing images. In this system, the plant ecological communities are defined with the inference of dominant species, physiognomy, and shared ecological settings by incorporating multiple strata. The DSPE system was implemented in a cool-temperate climate zone at a regional scale. The deep recurrent neural networks with bootstrap resampling method were employed for evaluating performance of the DSPE classification using Sentinel-2 images at 10 m spatial resolution. The performance of differentiating DSPE communities was compared with the differentiation of higher, Dominant Genus-Physiognomy-Ecological (DGPE) communities. Overall, there was a small difference in the classification between 58 DSPE communities (F1-score = 85.5%, Kappa coefficient = 84.7%) and 45 DGPE communities (F1-score = 86.5%, Kappa coefficient = 85.7%). However, the class wise accuracy analysis showed that all 58 DSPE communities were differentiated with more than 60% accuracy, whereas more than 70% accuracy was obtained for the classification of all 45 DGPE communities. Since all 58 DSPE communities were classified with more than 60% accuracy, the DSPE classification system was still effective for the differentiation of plant ecological communities from satellite images at a regional scale, indicating its applications in other regions in the world. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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16 pages, 546 KiB

Open AccessArticle

Ozonized Oleic Acid as a New Viticultural Treatment? Study of the Effect of LIQUENSO^® Oxygenate on the Carpoplane Microbial Community and Wine Microorganisms Combining Metabarcoding and In Vitro Assays

by Lea Franziska Stahl, Manon Edo, Timon Nonnenmacher, Daniela Reif, Friederike Rex, Pascal Wegmann-Herr, Andreas Kortekamp, Jochen Fischer-Schuch, Eckhard Thines and Maren Scharfenberger-Schmeer

Ecologies 2022, 3(3), 292-307; https://doi.org/10.3390/ecologies3030023 - 29 Jul 2022

Cited by 2 | Viewed by 2150

Abstract

In this study, an amplicon metagenomic approach was used to determine the effect of repeated treatments with ozonized oleic acid on the microbial community of grapevine carpoplane. Differences in community composition of treated vineyards were compared to non-treated and conventionally treated samples regarding [...] Read more.

In this study, an amplicon metagenomic approach was used to determine the effect of repeated treatments with ozonized oleic acid on the microbial community of grapevine carpoplane. Differences in community composition of treated vineyards were compared to non-treated and conventionally treated samples regarding the prokaryotic and eukaryotic microbiome at two developmental stages (BBCH 83, BBCH 87). The results showed effects both on occurrence and on abundance of microorganisms and the community assembly. Wine-relevant genera such as Acetobacter and members of the former genus Lactobacillus could be identified as part of the natural microbiota. The impact of the new viticultural treatment on these organisms was assessed in liquid culture-based microtiter assays. Therefore, we investigated an array of two acetic acid bacteria (AAB), four lactic acid bacteria (LAB) and nine saccharomyces and non-saccharomyces yeasts. Brettanomyces bruxellensis, Saccharomyces cerevisiae, Pediococcus sp. and Acetobacter aceti revealed the highest sensitivities against ozonized oleic acid (LIQUENSO^® Oxygenat). Culture growth of these organisms was significantly reduced at an ozonide concentration of 0.25% (v/v), which corresponded to a quarter of the concentration used in the vineyard. The metabarcoding approach in combination with complementary in vitro assays allow new insights into treatment effects on the community and species scale. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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11 pages, 1288 KiB

Open AccessArticle

A Comparison of Microbial Communities of Mango and Orange Residues for Bioprospecting of Biosurfactant Producers

by Fernanda de Paula, Natália Vama Vieira, Gabriela Fiori da Silva, Tiago Palladino Delforno and Iolanda Cristina Silveira Duarte

Ecologies 2022, 3(2), 120-130; https://doi.org/10.3390/ecologies3020010 - 20 May 2022

Cited by 3 | Viewed by 2318

Abstract

Plants and their derivatives, such as fruits, can be inhabited by different bacteria. However, this microbiota is still poorly studied. Among the wide variety of metabolites that bacteria produce, biosurfactants have been identified as potential molecules in the development of bioprocesses for various [...] Read more.

Plants and their derivatives, such as fruits, can be inhabited by different bacteria. However, this microbiota is still poorly studied. Among the wide variety of metabolites that bacteria produce, biosurfactants have been identified as potential molecules in the development of bioprocesses for various industrial sectors. In this work, we analyzed and compared the microbiota of fruit residues (mango and orange), in order to compare two possible sources of bioprospecting. For this, a bioinformatics approach was used to perform the taxonomic analysis and the prediction of the functional profile of the microbiota present in the samples. The results showed that the microbiota present in both fruit residues have the potential in biotechnological applications to produce biosurfactants, as these microbiota have genes related to the biosynthesis of these compounds. The common core of the microbiota present in the samples—Stenotrophomonas, Klebsiella, Serratia and Citrobacter—proved, according to the literature, to be composed of biosurfactant producers, showing the biosurfactant potential of the bacteria isolated from orange and mango residues. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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Review

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19 pages, 3988 KiB

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The Necrobiome of Deadwood: The Life after Death

by Roberta Pastorelli, Isabella De Meo and Alessandra Lagomarsino

Ecologies 2023, 4(1), 20-38; https://doi.org/10.3390/ecologies4010003 - 22 Dec 2022

Cited by 4 | Viewed by 4187

Abstract

In recent decades, sustainable forest management has been increasingly recognized, promoting the diffusion of silvicultural practices aimed at considering all components of the forest system. Deadwood is an important component of the forest ecosystem. It plays a fundamental role in providing nutrients and [...] Read more.

In recent decades, sustainable forest management has been increasingly recognized, promoting the diffusion of silvicultural practices aimed at considering all components of the forest system. Deadwood is an important component of the forest ecosystem. It plays a fundamental role in providing nutrients and habitats for a wide variety of saprotrophic and heterotrophic organisms and significantly contributes to soil formation and carbon storage. Deadwood is inhabited by a plethora of organisms from various kingdoms that have evolved the ability to utilize decaying organic matter. This community, consisting of both eukaryotic and prokaryotic species, can be defined as “necrobiome”. Through the interactions between its various members, the necrobiome influences the decay rates of deadwood and plays a crucial role in the balance between organic matter decomposition, carbon sequestration, and gas exchanges (e.g., CO₂) with the atmosphere. The present work aims to provide an overview of the biodiversity and role of the microbial communities that inhabit deadwood and their possible involvement in greenhouse gas (CO₂, N₂O, and CH₄) emissions. Full article

(This article belongs to the Special Issue Feature Papers of Ecologies 2022)

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