Research

14 pages, 3680 KiB

Open AccessArticle

DNA Barcode Gap Analysis for Multiple Marker Genes for Phytoplankton Species Biodiversity in Mediterranean Aquatic Ecosystems

by Eftychia Tzafesta, Benedetta Saccomanno, Francesco Zangaro, Maria Rosaria Vadrucci, Valeria Specchia and Maurizio Pinna

Biology 2022, 11(9), 1277; https://doi.org/10.3390/biology11091277 - 27 Aug 2022

Cited by 10 | Viewed by 2142

Abstract

The implementation of DNA metabarcoding and environmental DNA (eDNA) to the biodiversity assessment and biomonitoring of aquatic ecosystems has great potential worldwide. However, DNA metabarcoding and eDNA are highly reliant on the coverage of the DNA barcode reference libraries that are currently hindered [...] Read more.

The implementation of DNA metabarcoding and environmental DNA (eDNA) to the biodiversity assessment and biomonitoring of aquatic ecosystems has great potential worldwide. However, DNA metabarcoding and eDNA are highly reliant on the coverage of the DNA barcode reference libraries that are currently hindered by the substantial lack of reference sequences. The main objective of this study was to analyze the current coverage of DNA barcode reference libraries for phytoplankton species of the aquatic Mediterranean ecoregion in the southeast of Italy (Apulia Region) in order to assess the applicability of DNA metabarcoding and eDNA in this area. To do so, we investigated three main DNA barcode reference libraries, BOLD Systems, GenBank and SILVA, for the availability of DNA barcodes of the examined phytoplankton species. The gap analysis was conducted for three molecular gene markers, 18S, 16S and COI. The results showed a considerable lack of barcodes for all three markers. However, among the three markers, 18S had a greater coverage in the reference libraries. For the 18S gene marker, the barcode coverage gap across the three types of ecosystems examined was 32.21–39.68%, 60.12–65.19% for the 16S marker gene, and 72.44–80.61 for the COI marker gene. Afterwards, the interspecific genetic distance examined on the most represented molecular marker, 18S, was able to distinguish 80% of the species mined for lakes and 70% for both marine and transitional waters. Conclusively, this work highlights the importance of filling the gaps in the reference libraries, and constitutes the basis towards the advancement of DNA metabarcoding and eDNA application for biodiversity assessment and biomonitoring. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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17 pages, 1958 KiB

Open AccessArticle

Odonate Diversity Patterns in Italy Disclose Intricate Colonization Pathways

by Simone Fattorini

Biology 2022, 11(6), 886; https://doi.org/10.3390/biology11060886 - 08 Jun 2022

Cited by 4 | Viewed by 1632

Abstract

As a natural bridge between Europe and Africa, Italy occupies a prominent position to understand the biogeography of Europe. The influence of climatic, spatial, and historical factors on current patterns of species richness and turnover (i.e., inter-regional biogeographical differences) has been analyzed for [...] Read more.

As a natural bridge between Europe and Africa, Italy occupies a prominent position to understand the biogeography of Europe. The influence of climatic, spatial, and historical factors on current patterns of species richness and turnover (i.e., inter-regional biogeographical differences) has been analyzed for 88 species occurring in 17 Italian natural regions. Use of multimodel inference showed that odonate richness decreased southwards in response to decreasing rainfall, as expected for animals that depend on freshwater for their development. Use of Mantel tests indicated that patterns of inter-regional similarities were influenced by both climate and geographical distances. These patterns, as highlighted using Non-Metric Multidimensional Scaling, indicate a role for historical factors. Biogeographical similarities between Italian regions and adjacent areas revealed multiple colonization pathways. These results, coupled with the overall southward decrease in species richness, suggest that, after serving as a Pleistocene refuge from which odonates may have colonized medio-European areas, Italy was in turn subject to colonization from north to south. This resulted in Italian odonate fauna being less species rich compared to faunas in the medio-European territories, but also being biogeographically very complex. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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16 pages, 8473 KiB

Open AccessArticle

Factors Affecting Roadkills of Semi-Aquatic Mammals

by Linas Balčiauskas, Jos Stratford, Andrius Kučas and Laima Balčiauskienė

Biology 2022, 11(5), 748; https://doi.org/10.3390/biology11050748 - 13 May 2022

Cited by 3 | Viewed by 1682

Abstract

We previously showed that registration efforts and traffic intensity explain 90% of variation in mammal roadkill numbers, 70% of variation in the numbers of recorded species and 40% of diversity variation. Here we analyze semiaquatic mammal roadkill in Lithuania in 2002–2021, relating these [...] Read more.

We previously showed that registration efforts and traffic intensity explain 90% of variation in mammal roadkill numbers, 70% of variation in the numbers of recorded species and 40% of diversity variation. Here we analyze semiaquatic mammal roadkill in Lithuania in 2002–2021, relating these to the monitoring effort. From 39,936 analyzed roadkill, the European beaver (Castor fiber) was registered 60 times, American mink (Neovison vison) 26 times, otter (Lutra lutra) 22 times and muskrat (Ondatra zibethica) 3 times. The average roadkill indexes were 0.000065, 0.00076, 0.00061 and 0.00010 ind./km/day, and the extrapolated annual roadkill for the country was 44–357, 36–456, 49–464 and 89–144 individuals, respectively. Beaver roadkill numbers correlated with the registration effort and traffic intensity, otter roadkill with registration effort only and mink with hunting bag (number of hunted individuals per year). Roadkill was not always related to proximity to water, with 38–54% of roadkill occurring over 200 m from the nearest water source. With American mink and muskrat being invasive species in the EU and otter protected in many countries, it is valuable to enhance the registrations of their roadkill (using targeted efforts by drivers, hunters or other citizen scientists) to obtain the extrapolated amount of roadkill and to use this knowledge in species management. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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19 pages, 2698 KiB

Open AccessArticle

Coastal Mesozooplankton Assemblages during Spring Bloom in the Eastern Barents Sea

by Vladimir G. Dvoretsky and Alexander G. Dvoretsky

Biology 2022, 11(2), 204; https://doi.org/10.3390/biology11020204 - 27 Jan 2022

Cited by 11 | Viewed by 2305

Abstract

Mesozooplankton play an important role in Arctic shelf ecosystems as a trophic link and a key food source for many larval fish species. The distribution of mesozooplankton in the eastern Barents Sea was studied along a 500 nautical mile-long transect in May 2016 [...] Read more.

Mesozooplankton play an important role in Arctic shelf ecosystems as a trophic link and a key food source for many larval fish species. The distribution of mesozooplankton in the eastern Barents Sea was studied along a 500 nautical mile-long transect in May 2016 during the spring bloom. Mesozooplankton were sampled using a Juday net hauled from the surface to the bottom at 12 stations. We found good correspondence between the distribution of water masses and mesozooplankton assemblages. Mesozooplankton abundance (mean 73·10³ individuals m⁻²) in Novaya Zemlya coastal water was dominated by Copepoda ova and nauplii, Thyssanoessa spp. nauplii and Oithona similis. Parasagitta elegans and Calanus finmarchicus comprised most of the total mesozooplankton biomass (mean 0.9 g dry mass m⁻²) in that water mass. A second assemblage (mean abundance 171·10³ individuals m⁻²) was associated with the colder Barents Sea water, with Oithona similis, Copepoda nauplii, Fritillaria borealis and Cirripedia nauplii being the most numerous. In that water mass, C. finmarchicus, Metridia longa, Cirripedia nauplii and Calanus glacialis contributed most to the total biomass (mean 3 g dry mass m⁻²). The dominance of young stages of Copepoda and a high proportion of meroplankton were typical of spring mesozooplankton assemblages. The spatial distribution of mesozooplankton abundance and biomass was strongly correlated with latitude, longitude and chlorophyll a concentration, which together explained 10% of the total variance in mesozooplankton density. The present investigation is a baseline study for the assessment of the spring mesozooplankton assemblage in the eastern Barents Sea, and for an evaluation of the possible impact of future environmental changes on the Arctic shelf marine ecosystem. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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14 pages, 2913 KiB

Open AccessArticle

Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar

by Olga Kostyunina, Aleksei Traspov, Alexander Economov, Ivan Seryodkin, Aleksandr Senchik, Neckruz Bakoev, Yuri Prytkov, Nikolay Bardukov, Igor Domsky and Tatiana Karpushkina

Biology 2022, 11(2), 203; https://doi.org/10.3390/biology11020203 - 27 Jan 2022

Cited by 3 | Viewed by 2654

Abstract

The wild boar is the wild ancestor of the domestic pig and one of the most common species of ungulates. At the beginning of the 20th century, the wild boar was practically exterminated in the European part of Russia. In the period 1935–1988, [...] Read more.

The wild boar is the wild ancestor of the domestic pig and one of the most common species of ungulates. At the beginning of the 20th century, the wild boar was practically exterminated in the European part of Russia. In the period 1935–1988, 7705 boars were caught in various regions of the European part of Russia, the Far East, Ukraine, Belarus, Kyrgyzstan, Kazakhstan, Latvia, Lithuania, Estonia, Tajikistan and resettled in the territory of Russia. Asian and European wild boars dwell the territory of Russia. The aim of our research was to study the genetic diversity and structure of wild boar populations in different regions of Russia using genome-wide genotyping. We have determined the genetic distances, population structure, parameters of genetic diversity and significantly expanded our understanding of the genetic state of the Russian wild boar. For the first time, we calculated autozygosity of the wild boar of the European and Asian subspecies using Homozygous-by-Descent (HBD) Segments analysis, which is important in terms of population recovery. We also found evidence of hybridization between Russian wild boar and domestic pigs. A group of European wild boars showed introgression of the Asian boar into population. The mean level of the inbreeding coefficient in European wild boar was higher than in Asian wild boar, and combined groups of the European boar had higher inbreeding coefficient than Russian wild boars. These results obtained can be used in population management. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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19 pages, 3140 KiB

Open AccessArticle

Soil Bacterial Community Shifts Are Driven by Soil Nutrient Availability along a Teak Plantation Chronosequence in Tropical Forests in China

by Zhi Yu, Kunnan Liang, Guihua Huang, Xianbang Wang, Mingping Lin, Yinglong Chen and Zaizhi Zhou

Biology 2021, 10(12), 1329; https://doi.org/10.3390/biology10121329 - 15 Dec 2021

Cited by 17 | Viewed by 2670

Abstract

Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and [...] Read more.

Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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18 pages, 9351 KiB

Open AccessArticle

Response of Annual Herbaceous Plant Leaching and Decomposition to Periodic Submergence in Mega-Reservoirs: Changes in Litter Nutrients and Soil Properties for Restoration

by Xin Hu, Tingting Xie, Muhammad Arif, Dongdong Ding, Jiajia Li, Zhongxun Yuan and Changxiao Li

Biology 2021, 10(11), 1141; https://doi.org/10.3390/biology10111141 - 05 Nov 2021

Cited by 15 | Viewed by 1764

Abstract

Litter decomposition is an important soil nutrient source that promotes vegetation in deteriorated riparian zones worldwide. The periodic submergence and sediment burial effects on two prominent annual herbaceous plants (Echinochloa crusgali and Bidens tripartite) are little known in mega-reservoir settings. Our [...] Read more.

Litter decomposition is an important soil nutrient source that promotes vegetation in deteriorated riparian zones worldwide. The periodic submergence and sediment burial effects on two prominent annual herbaceous plants (Echinochloa crusgali and Bidens tripartite) are little known in mega-reservoir settings. Our study focuses on the mass and carbon loss and nutrient release from E. crusgali and B. tripartitle litter and changes in soil properties, which are important for riparian zone rehabilitation in the Three Gorges Dam Reservoir, China. This study adopted the litter bag method to explore the nutrient change characteristics and changes in soil properties at different sediment burial depths under flooding scenarios. Three burial depths (0 cm, 5 cm, and 10 cm) were used for these two plants, and the experiment lasted for 180 days. The results revealed that the litter decay rate was high at first in the incubation experiment, and the nutrient loss rate followed the pattern of K > P > N > C. The relationship between % C remaining and % mass remaining was nearly 1:1, and the total amount of P exhibited a leaching–enrichment–release state in the decomposition process. Nutrients were changed significantly in the soil and overlying water at the first decomposition stage. Still, the total soil nutrient change was insignificant at the end, except for the 10 cm burial of B. tripartitle. Moreover, oxidation–reduction potential was the main factor in the litter decomposition process at different burial depths. This study indicated that sediment deposition reduced litter mass loss, slowed down the release of N and P, and retained more C, but promoted the release of K. Conclusively, in litter decomposition under waterlogging, the total soil nutrient content changed little. However, litter does more to the soil than that. Therefore, it is necessary to study the residual soil litter’s continuous output after the water level declines for restoration purposes. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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17 pages, 4925 KiB

Open AccessArticle

Amazing Discoveries of Benthic Fauna from the Abyssal Zone of Lake Baikal

by Ilya G. Kondratov, Tatiana Ya. Sitnikova, Irina A. Kaygorodova, Natalia N. Denikina, Vadim V. Annenkov, Igor V. Khanaev, Sergei V. Kirilchik, Ivan A. Nebesnykh and Elena V. Dzyuba

Biology 2021, 10(10), 972; https://doi.org/10.3390/biology10100972 - 27 Sep 2021

Cited by 2 | Viewed by 2208

Abstract

Lake Baikal is a natural laboratory for the study of species diversity and evolution, as a unique freshwater ecosystem meeting the all of the main criteria of the World Heritage Convention. However, despite many years of research, the true biodiversity of the lake [...] Read more.

Lake Baikal is a natural laboratory for the study of species diversity and evolution, as a unique freshwater ecosystem meeting the all of the main criteria of the World Heritage Convention. However, despite many years of research, the true biodiversity of the lake is clearly insufficiently studied, especially that of deep-water benthic sessile organisms. For the first time, plastic waste was raised from depths of 110 to 190 m of Lake Baikal. The aim of this study was to examine the biological community inhabiting the plastic substrate using morphological and molecular genetic analysis. Fragments of plastic packaging materials were densely populated: bryozoans, leeches and their cocoons, capsules of gastropod eggs, and turbellaria cocoons were found. All the data obtained as a result of an analysis of the nucleotide sequences of the standard bar-coding fragment of the mitochondrial genome turned out to be unique. Our results demonstrate the prospects for conducting comprehensive studies of artificial substrates to determine the true biodiversity of benthos in the abyssal zone of Lake Baikal. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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22 pages, 2267 KiB

Open AccessArticle

Response of Aquatic Organisms Communities to Global Climate Changes and Anthropogenic Impact: Evidence from Listvennichny Bay of Lake Baikal

by Lyubov Kravtsova, Svetlana Vorobyeva, Elena Naumova, Lyudmila Izhboldina, Elena Mincheva, Tatyana Potemkina, Galina Pomazkina, Elena Rodionova, Natalya Onishchuk, Mariya Sakirko, Ivan Nebesnykh and Igor Khanaev

Biology 2021, 10(9), 904; https://doi.org/10.3390/biology10090904 - 13 Sep 2021

Cited by 11 | Viewed by 2500

Abstract

Recent studies have revealed how the freshwater biota of Lake Baikal responds to climate change and anthropogenic impacts. We studied phyto- and zooplankton, as well as phyto- and zoobenthos, in the open coastal waters of the southern basin of the lake and of [...] Read more.

Recent studies have revealed how the freshwater biota of Lake Baikal responds to climate change and anthropogenic impacts. We studied phyto- and zooplankton, as well as phyto- and zoobenthos, in the open coastal waters of the southern basin of the lake and of Listvennichny Bay. A total of 180 aquatic organism taxa were recorded. The response of the Baikal ecosystem to climate change can be traced by changes in the species composition of planktonic communities of the lake’s open coasts in summer. The key species were thermophilic the Anabaena lemmermannii P. Richt. (F_ij = +0.7) blue-green algae, the Asplanchna priodonta Gosse (F_ij = +0.6) rotifers in 2016, the Rhodomonas pusilla (Bachm.) Javorn. (F_ij = +0.5) cold-loving algae, and the Cyclops kolensis Lilljeborg (F_ij = +0.9) copepods in the past century. The proportion of Chlorophyta decreased from 63% to 17%; the Cyanophyta increased from 3% to 11% in the total biomass of phytoplankton; and the proportion of Cladocera and Rotifera increased to 26% and 11% in the biomass of zooplankton, respectively. Human activity makes an additional contribution to the eutrophication of coastal waters. The Dinobryon species, the cosmopolitan Asterionella formosa Hass. and Fragilaria radians Kütz., dominated phytoplankton, and filamentous algae, Spirogyra, dominated at the bottom in the area with anthropogenic impact. The trophic level was higher than at the unaffected background site: the saprobity index varied from 1.45 to 2.17; the ratio of eutrophic species to oligotrophic species ranged from 1:2 to 3:1, and the ratio of mesosaprobiont biomass to endemics biomass ranged from 2:1 to 7:1. Currently, the boundaries of eutrophication zones of shallow waters in Lake Baikal are expanding, and its coastal zone has acquired features typical of freshwater bodies of the eutrophic type. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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22 pages, 5365 KiB

Open AccessArticle

Artificial Plantation Responses to Periodic Submergence in Massive Dam and Reservoir Riparian Zones: Changes in Soil Properties and Bacterial Community Characteristics

by Jiajia Li, Lijuan Li, Muhammad Arif, Dongdong Ding, Xin Hu, Jie Zheng, Zhongxun Yuan and Changxiao Li

Biology 2021, 10(8), 819; https://doi.org/10.3390/biology10080819 - 23 Aug 2021

Cited by 19 | Viewed by 2659

Abstract

Plant and microbiome interactions are necessary for plant nutrient acquisition. However, relatively little is known about the responses of roots, bulk, and rhizosphere soil microbial communities in different artificial vegetation types (woody and herbaceous) in riparian areas of massive dams and reservoirs. Therefore, [...] Read more.

Plant and microbiome interactions are necessary for plant nutrient acquisition. However, relatively little is known about the responses of roots, bulk, and rhizosphere soil microbial communities in different artificial vegetation types (woody and herbaceous) in riparian areas of massive dams and reservoirs. Therefore, this study aims to assess such responses at elevations of 165–170 m a.s.l. in the riparian zones of the Three Gorges Dam Reservoir, China. The samples were collected containing the rhizosphere soil, bulk soil, and roots of herbaceous and woody vegetation at different emergence stages in 2018. Then, all the samples were analyzed to quantify the soil properties, bacterial community characteristics, and their interaction in the early and late emergence phases. In different periods, the weight of dominant soil bacteria, including Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Cyanobacteria, was higher, and their composition was different in the rhizosphere, bulk soil, and endophytes. Moreover, the soil co-occurrence networks indicated that the weight of soil physical properties was higher than chemical properties in the early emergence stage. In contrast, the weight of chemical properties was relatively higher in the late emergence stage. Furthermore, the richness and diversity of the bacterial community were mainly affected by soil organic matter. This study suggests that these herbaceous and woody vegetation are suitable for planting in reservoir areas affected by hydrology and human disturbance in light of soil nutrients and soil microbial communities, respectively. Additionally, these results provide valuable information to inoculate the soil with key microbiota members by applying fertilizers, potentially improving plant health and soil production. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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22 pages, 3942 KiB

Open AccessArticle

Comparison of Diazotrophic Composition and Distribution in the South China Sea and the Western Pacific Ocean

by Changling Ding, Chao Wu, Liuyang Li, Laxman Pujari, Guicheng Zhang and Jun Sun

Biology 2021, 10(6), 555; https://doi.org/10.3390/biology10060555 - 20 Jun 2021

Cited by 5 | Viewed by 2650

Abstract

The variation of diazotrophs has been elusive in multiple SCS and WPO regions due to insufficient data. Therefore, the dynamics of diazotrophic composition and distribution were investigated in this study, based on high-throughput sequencing and quantitative PCR of the nifH gene. We found [...] Read more.

The variation of diazotrophs has been elusive in multiple SCS and WPO regions due to insufficient data. Therefore, the dynamics of diazotrophic composition and distribution were investigated in this study, based on high-throughput sequencing and quantitative PCR of the nifH gene. We found that Proteobacteria dominated the diazotrophic community in the river-impacted SCS and cyanobacteria and Proteobacteria were more abundant in the ocean-dominated SCS and WPO. The qPCR analysis showed that cyanobacterial Trichodesmium was abundant in the Pearl River plume and in the SCS basin influenced by the Kuroshio intrusion, and it also thrived in the subequatorial region of the WPO. Unicellular cyanobacteria UCYN-A were mainly detected in the river-impacted area, UCYN-B was abundant in the WPO, UCYN-C had a relatively high abundance in the ocean-dominated area, and a preponderance of γ-Proteobacteria γ-24774A11 was observed in the ocean-dominated SCS and pelagic WPO. Diazotrophic communities had significant distance–decay relationships, reflecting clear biogeographic patterns in the study area. The variations of diazotrophic community structure were well explained by dissolved inorganic nitrogen, dissolved inorganic phosphate by an eigenvector spatial variable PCNM1. These results provide further information to help determine the ecological mechanism of elusive diazotrophic communities in different ocean ecosystems. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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15 pages, 21458 KiB

Open AccessArticle

The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean

by Changling Ding, Chao Wu, Congcong Guo, Jiang Gui, Yuqiu Wei and Jun Sun

Biology 2021, 10(3), 248; https://doi.org/10.3390/biology10030248 - 22 Mar 2021

Cited by 6 | Viewed by 2494

Abstract

Currently, there is scant information about the biodiversity and functional diversity of microbes in the eastern Indian Ocean (EIO). Here, we used a combination of high-throughput sequencing of 16S rRNA genes and a metagenomic approach to investigate the microbial population structure and its [...] Read more.

Currently, there is scant information about the biodiversity and functional diversity of microbes in the eastern Indian Ocean (EIO). Here, we used a combination of high-throughput sequencing of 16S rRNA genes and a metagenomic approach to investigate the microbial population structure and its metabolic function in the equatorial EIO. Our results show that Cyanobacterial Prochlorococcus made up the majority of the population. Interestingly, there were fewer contributions from clades SAR11 (Alphaproteobacteria) and SAR86 (Gammaproteobacteria) to microbial communities than contributions from Prochlorococcus. Based on functional gene analysis, functional genes rbcL, narB, and nasA were relatively abundant among the relevant genes. The abundance of Prochlorococcus implies its typically ecological adaptation in the local ecosystem. The microbial metabolic potential shows that in addition to the main carbon fixation pathway Calvin cycle, the rTCA cycle and the 3-HP/4-HB cycle have potential alternative carbon fixation contributions to local ecosystems. For the nitrogen cycle, the assimilatory nitrate and nitrite reduction pathway is potentially the crucial form of nitrogen utilization; unexpectedly, nitrogen fixation activity was relatively weak. This study extends our knowledge of the roles of microbes in energy and resource cycling in the EIO and provides a foundation for revealing profound biogeochemical processes driven by the microbial community in the ocean. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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19 pages, 3117 KiB

Open AccessArticle

Predicting Hotspots and Prioritizing Protected Areas for Endangered Primate Species in Indonesia under Changing Climate

by Aryo Adhi Condro, Lilik Budi Prasetyo, Siti Badriyah Rushayati, I Putu Santikayasa and Entang Iskandar

Biology 2021, 10(2), 154; https://doi.org/10.3390/biology10020154 - 15 Feb 2021

Cited by 20 | Viewed by 5939

Abstract

Indonesia has a large number of primate diversity where a majority of the species are threatened. In addition, climate change is conservation issues that biodiversity may likely face in the future, particularly among primates. Thus, species-distribution modeling was useful for conservation planning. Herein, [...] Read more.

Indonesia has a large number of primate diversity where a majority of the species are threatened. In addition, climate change is conservation issues that biodiversity may likely face in the future, particularly among primates. Thus, species-distribution modeling was useful for conservation planning. Herein, we present protected areas (PA) recommendations with high nature-conservation importance based on species-richness changes. We performed maximum entropy (Maxent) to retrieve species distribution of 51 primate species across Indonesia. We calculated species-richness change and range shifts to determine the priority of PA for primates under mitigation and worst-case scenarios by 2050. The results suggest that the models have an excellent performance based on seven different metrics. Current primate distributions occupied 65% of terrestrial landscape. However, our results indicate that 30 species of primates in Indonesia are likely to be extinct by 2050. Future primate species richness would be also expected to decline with the alpha diversity ranging from one to four species per 1 km². Based on our results, we recommend 54 and 27 PA in Indonesia to be considered as the habitat-restoration priority and refugia, respectively. We conclude that species-distribution modeling approach along with the categorical species richness is effectively applicable for assessing primate biodiversity patterns. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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14 pages, 3009 KiB

Open AccessArticle

Microbial Characteristics and Safety of Dairy Manure ComPosting for Reuse as Dairy Bedding

by Haoming Wu, Yang Wang, Lei Dong, Haiyan Hu, Lu Meng, Huimin Liu, Nan Zheng and Jiaqi Wang

Biology 2021, 10(1), 13; https://doi.org/10.3390/biology10010013 - 28 Dec 2020

Cited by 9 | Viewed by 2611

Abstract

Changes in bacterial community, phenotype, metabolic function, and pathogenic bacteria content in recycled manure solids (RMS) were analyzed by 16S rRNA sequencing, Bugbase, picrost2, and qPCR, respectively. The data from RMS bedding were compared to those of sand bedding and rice husk bedding. [...] Read more.

Changes in bacterial community, phenotype, metabolic function, and pathogenic bacteria content in recycled manure solids (RMS) were analyzed by 16S rRNA sequencing, Bugbase, picrost2, and qPCR, respectively. The data from RMS bedding were compared to those of sand bedding and rice husk bedding. The results show that the proportion of potentially pathogenic bacteria among the manure flora of RMS after dry and wet separation, after composting, and after sun-cure storage was 74.00%, 26.03%, and 49.067%, respectively. Compared to RMS bedding, the proportion of potentially pathogenic microorganisms in sand bedding and rice husk bedding was higher. The picrust2 analyses show that the level of lipopolysaccharide biosynthesis changed significantly during RMS processing. In addition, the qPCR results show that composting could effectively reduce the detection and quantification of pathogens, except Streptococcus uberis, in RMS bedding. In general, composting is an essential step to improve the safety of bedding materials in the process of fecal treatment. However, at the same time, RMS bedding may increase the risk of mastitis caused by Streptococcus uberis. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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