scholarly journals From microbes to mammals: agriculture homogenizes pond biodiversity across different land-use types

2021 ◽  
Vol 4 ◽  
Author(s):  
Danny Ionescu ◽  
Mina Bizic ◽  
Rajat Karnatak ◽  
Camille Musseau ◽  
Gabriela Onandia ◽  
...  
Keyword(s):  
Land Use ◽  
Taxonomic Diversity ◽  
Amplicon Sequencing ◽  
Agricultural Landscapes ◽  
Intensive Agriculture ◽  
Rrna Genes ◽  
High Quality ◽  
Biodiversity Patterns ◽  
Land Use Types ◽  
Taxonomic Groups

The diversity and composition of biological communities in ecosystems is typically linked to land use. Consequently, intensive agriculture has a strong influence on these patterns, including a reduction and homogenization of species diversity. Kettle holes (KH; also known as potholes) are small water bodies (<1 ha) typical to formerly glaciated land on the northern hemisphere, reaching densities up to several dozen per km2. They often function as drainage centers, linking various landscape elements in their surroundings and are hotspots of aquatic biodiversity in terrestrial landscapes. In the 1950s, the land use surrounding KH in Europe (e.g., Germany, Poland, The Netherlands) and North America (USA and Canada) shifted towards intensive agriculture, likely affecting the local and regional biodiversity of the KH. Reports on the biodiversity of ponds in agricultural landscapes are scarce, and mostly focus on single taxa. We used deep eDNA amplicon sequencing of eukaryotic, bacterial, and archaeal SSU rRNA genes to assess effects of land use on the overall species biodiversity of 67 KH in either arable fields, grasslands, or forests, all embedded in a landscape subjected to intensive agriculture for decades. These were later contrasted with Berlin city ponds. Metatranscriptomic analyses were conducted in parallel to investigate the taxonomic diversity and functionality of the active communities. The amplicon data, >300 million reads, were analyzed with phyloFlash and Kraken2 using the SILVA_SSU_Ref database. Subsequently, the sequences were grouped based on taxonomy. The use of different annotation pipelines resulted in similar patterns. A subset of the data was analyzed using DADA2, generating amplicon sequence variants. Clustering the sequences as variants or according to taxonomy resulted in identical patterns, suggesting that broad taxonomical groupings provide sufficient resolution for general overviews. Annotation of the eukaryotic community was challenging, as none of the currently available databases contains sufficient high-quality sequences to cover the entire phylogenetic breadth. To overcome this limitation, we used the SILVA_SSU_Parc database, which also contains short sequences excluded from SILVA_SSU_Ref, thus extending the taxonomic base of the analysis. The curated, high-quality PR2 eukaryotic database did not provide better results than the SILVA_SSU_Ref database. An incompatibility between the SILVA and classical taxonomic nomenclature resulted in a ‘language barrier,’ which could be partly resolved by using the parallel EMBL taxonomy provided in the SILVA databases. Nevertheless, we propose that short-read SSU-based eukaryotic taxonomic annotations should be validated by other means. Despite such methodological limitations, our study demonstrates that deep amplicon sequencing of eDNA return a reliable picture of the biodiversity in complex ecosystems. Such information is sufficient to identify biodiversity patterns across the three domains of life and can serve to pinpoint taxonomic groups which should be investigated by a more detailed approach. Our study concluded that long-term exposure to intensive agriculture results in biodiversity homogenization across diverse taxonomic groups, removing most differences in biodiversity patterns among land-use types. This outcome contrasts with biodiversity patterns associated with sediments of the KH, where temporal coverage by the eDNA analyses extends back to at least the onset of intensive agriculture. However, metatranscriptomic analyses, reflecting the distribution of activities rather than relative abundance, revealed temporal differences in the structure of the active community in KH of the investigated land-use types, matching times of field fertilization. Thus, even in a landscape where biodiversity has been homogenized, inputs from the surroundings result in short-term activity changes of different organisms. This needs to be considered when developing new management schemes needed to counteract the current biodiversity loss.

scholarly journals Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Caitlin M. Singleton ◽  
Francesca Petriglieri ◽  
Jannie M. Kristensen ◽  
Rasmus H. Kirkegaard ◽  
Thomas Y. Michaelsen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Wastewater Treatment Plants ◽  
In Situ Hybridisation ◽  
Amplicon Sequencing ◽  
Rrna Genes ◽  
Fluorescence In Situ Hybridisation ◽  
Sequencing Data ◽  
High Quality ◽  
16S Rrna Amplicon Sequencing ◽  
Long Read

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

scholarly journals Eukaryotic Microbial Communities in Japanese Arable Andisols Investigated by Amplicon Sequencing of 18S rRNA Genes

2020 ◽  
Vol 9 (23) ◽  
Author(s):  
Kazumori Mise ◽  
Shigeto Otsuka
Keyword(s):  
Microbial Communities ◽  
18S Rrna ◽  
Amplicon Sequencing ◽  
Rrna Genes ◽  
Community Structures ◽  
Arable Soils ◽  
Eukaryotic Community ◽  
Taxonomic Groups ◽  
18S Rrna Genes

ABSTRACT Compared with the well-studied soil prokaryotic communities, little is known about soil eukaryotic communities. Here, we investigated the eukaryotic community structures in 43 arable soils using amplicon sequencing of 18S rRNA genes. Major taxonomic groups, such as Fungi, Holozoa, and Stramenopiles, were detected in all samples.

scholarly journals Global effects of land-use intensity on local pollinator biodiversity

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joseph Millard ◽  
Charlotte L. Outhwaite ◽  
Robyn Kinnersley ◽  
Robin Freeman ◽  
Richard D. Gregory ◽  
...  
Keyword(s):  
Land Use ◽  
Land Use Intensity ◽  
Beneficial Effects ◽  
Land Use Types ◽  
Tropical Areas ◽  
Low Levels ◽  
Taxonomic Groups ◽  
The Tropics ◽  
Effects Of Land Use ◽  
Urban Sites

AbstractPollinating species are in decline globally, with land use an important driver. However, most of the evidence on which these claims are made is patchy, based on studies with low taxonomic and geographic representativeness. Here, we model the effect of land-use type and intensity on global pollinator biodiversity, using a local-scale database covering 303 studies, 12,170 sites, and 4502 pollinating species. Relative to a primary vegetation baseline, we show that low levels of intensity can have beneficial effects on pollinator biodiversity. Within most anthropogenic land-use types however, increasing intensity is associated with significant reductions, particularly in urban (43% richness and 62% abundance reduction compared to the least intensive urban sites), and pasture (75% abundance reduction) areas. We further show that on cropland, the strongly negative response to intensity is restricted to tropical areas, and that the direction and magnitude of response differs among taxonomic groups. Our findings confirm widespread effects of land-use intensity on pollinators, most significantly in the tropics, where land use is predicted to change rapidly.

scholarly journals Diversity of Indigenous Woody Species in Small Holder Farm Lands: Comparison across Different Agroecology and Land Use Types in Chilga and Dabat District, Northern Ethiopia

2018 ◽  
Vol 6 (08) ◽  
Author(s):  
Dagm Fikir Abate ◽  
Mekuannint Tebikew ◽  
Yohannis Gebremariam
Keyword(s):  
Land Use ◽  
Tree Species ◽  
Woody Species ◽  
Agricultural Landscapes ◽  
Indigenous Species ◽  
Stem Number ◽  
Land Use Types ◽  
Native Tree ◽  
Native Tree Species ◽  
Different Parts

Ethiopia is known for its massive expansion of plantations and woodlots, that are mainly of monocultures of the exotic tree species, Eucalyptus, which has still remained the pre-dominant tree components of plantations as well as farming systems in different parts of Ethiopian highlands, including the highlands in North Gondar. However, the status of indigenous/native tree species in these areas has become very limited, and is considered at risk. The current study was conducted in Chiliga and Dabat districts of North Gondar zone; it assessed (i) indigenous woody species diversity of farmlands in different agro-ecologies and farm land use categories, (ii) management and conservation practices carried out by farmers, and (iii) major constraints for enhancing on-farm integration of indigenous woody species. Primary data was obtained using such methods as, formal household survey, group discussion, observation and woody species inventory in two villages selected randomly from highland and mid highland for Dabat, and mid land and lowland for Chiliga district. A complete census of all woody individuals was conducted on all plots/parcels of 80 households. A total of 35 species were encountered in the farm lands of the studied area. Six of the total species was exotic, and constitute about 85% of the total abundance. The number of woody species per household increased with decreased agroecological gradient, and the largest value of stem number was found at the highland, followed by at mid highland, whereas least stem number was found in the lowland site. Likewise, the study found that homegardens host more diverse indigenous species than other land use types. Even though farm lands in the study areas were home to different indigenous woody species higher in number than exotic species, it was possible to confirm the already reported evidence that revealed exotic species have been remaining the pre-dominant tree components of the agricultural landscapes in different parts of Ethiopian highlands. However, the fact that remnant native tree individuals are currently growing with in the agricultural landscapes is an indication of the opportunity for integrating and managing native tree species through Agroforestry systems. The study concludes that there is a considerable possibilities of native and indigenous species to exist as an integral component of agricultural land use systems in Northern highlands where Eucalyptus expansion has remained the main focus of research and extension efforts.

scholarly journals Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period

2021 ◽  
Vol 12 ◽  
Author(s):  
Suhyun Kim ◽  
Md. Rashedul Islam ◽  
Ilnam Kang ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
High Throughput ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Taxonomic Groups ◽  
Bacterial Groups

Although many culture-independent molecular analyses have elucidated a great diversity of freshwater bacterioplankton, the ecophysiological characteristics of several abundant freshwater bacterial groups are largely unknown due to the scarcity of cultured representatives. Therefore, a high-throughput dilution-to-extinction culturing (HTC) approach was implemented herein to enable the culture of these bacterioplankton lineages using water samples collected at various seasons and depths from Lake Soyang, an oligotrophic reservoir located in South Korea. Some predominant freshwater bacteria have been isolated from Lake Soyang via HTC (e.g., the acI lineage); however, large-scale HTC studies encompassing different seasons and water depths have not been documented yet. In this HTC approach, bacterial growth was detected in 14% of 5,376 inoculated wells. Further, phylogenetic analyses of 16S rRNA genes from a total of 605 putatively axenic bacterial cultures indicated that the HTC isolates were largely composed of Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. Importantly, the isolates were distributed across diverse taxa including phylogenetic lineages that are widely known cosmopolitan and representative freshwater bacterial groups such as the acI, acIV, LD28, FukuN57, MNG9, and TRA3–20 lineages. However, some abundant bacterial groups including the LD12 lineage, Chloroflexi, and Acidobacteria could not be domesticated. Among the 71 taxonomic groups in the HTC isolates, representative strains of 47 groups could either form colonies on agar plates or be revived from frozen glycerol stocks. Additionally, season and water depth significantly affected bacterial community structure, as demonstrated by 16S rRNA gene amplicon sequencing analyses. Therefore, our study successfully implemented a dilution-to-extinction cultivation strategy to cultivate previously uncultured or underrepresented freshwater bacterial groups, thus expanding the basis for future multi-omic studies.

scholarly journals Horizontal and vertical species turnover in tropical birds in habitats with differing land use

2017 ◽  
Vol 13 (5) ◽  
pp. 20170186 ◽  
Author(s):  
Rachakonda Sreekar ◽  
Richard T. Corlett ◽  
Salindra Dayananda ◽  
Uromi Manage Goodale ◽  
Adam Kilpatrick ◽  
...  
Keyword(s):  
Land Use ◽  
Species Turnover ◽  
Bird Species ◽  
Forest Edge ◽  
Intensive Agriculture ◽  
Primary Forest ◽  
Turnover Rates ◽  
Forest Reserve ◽  
Land Use Types ◽  
Elevational Range

Large tracts of tropical rainforests are being converted into intensive agricultural lands. Such anthropogenic disturbances are known to reduce species turnover across horizontal distances. But it is not known if they can also reduce species turnover across vertical distances (elevation), which have steeper climatic differences. We measured turnover in birds across horizontal and vertical sampling transects in three land-use types of Sri Lanka: protected forest, reserve buffer and intensive-agriculture, from 90 to 2100 m a.s.l. Bird turnover rates across horizontal distances were similar across all habitats, and much less than vertical turnover rates. Vertical turnover rates were not similar across habitats. Forest had higher turnover rates than the other two habitats for all bird species. Buffer and intensive-agriculture had similar turnover rates, even though buffer habitats were situated at the forest edge. Therefore, our results demonstrate the crucial importance of conserving primary forest across the full elevational range available.

scholarly journals Land use temporarily affects active pond-community structure but not gene expression patterns

2021 ◽  
Author(s):  
Mina Bizic ◽  
Danny Ionescu ◽  
Rajat Karnatak ◽  
Camille Musseau ◽  
Gabriela Onandia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Land Use ◽  
Community Structure ◽  
Expression Patterns ◽  
Agricultural Landscapes ◽  
Water Bodies ◽  
Intensive Agriculture ◽  
Gene Expression Patterns ◽  
Land Use Type ◽  
Northeastern Germany

Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics, to understand the responses of active communities across the three domains of life, Bacteria, Archaea, and eukaryotes, to land use. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel eDNA study which revealed the homogenization of biodiversity across KH conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced in eukaryotes than in bacteria. In contrast, gene expression patterns did not differ between months or across land-use type, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active community structure, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results show that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.

scholarly journals Differential responses of amphibians and reptiles to land-use change in the biodiversity hotspot of north-eastern Madagascar

2021 ◽  
Author(s):  
Thio Rosin Fulgence ◽  
Dominic Andreas Martin ◽  
Romual Randriamanantena ◽  
Ronick Botra ◽  
Erosiniot Befidimanana ◽  
...  
Keyword(s):  
Land Use ◽  
Species Richness ◽  
Land Use Change ◽  
Agricultural Landscapes ◽  
Old Growth ◽  
Forest Dependency ◽  
Old Growth Forest ◽  
Land Use Types ◽  
Reptile Species ◽  
North Eastern

Large expanses of tropical rainforest have been converted into agricultural landscapes cultivated by smallholder farmers. This is also the case in north-eastern Madagascar; a region that retains a significant proportions of forest cover despite shifting hill rice cultivation and vanilla agroforestry. The region is also a global hotspot for herpetofauna diversity, but how this diversity is affected by land-use change remains largely unknown. Using a space-for-time study design to uncover land-use effects, we compared species diversity and community composition in seven prevalent land uses: unburned (old-growth forest, forest fragment, and forest-derived vanilla agroforest) and burned (fallow-derived vanilla agroforest, woody fallow, herbaceous fallow) land-use types, and rice paddy. We conducted six comprehensives, time-standardized searches across at least ten replicates of each land-use type and applied genetic barcoding to confirm species identification. We documented an outstanding diversity of endemic herpetofauna (119 species): amphibian species richness at the plot level was highest in old-growth forest and significantly lower in all other land-use types. Plot-level reptile species richness was significantly higher in the unburned land-use types than burned land-use types. For both amphibians and reptiles, the less-disturbed land-use types showed more uneven communities and particularly in old-growth forest, the species composition differed significantly from all other land-use types. Amphibians showed a higher level of forest dependency compared to reptiles (38% versus 28% of species exclusively occurred in old-growth forest). Our analyses thus revealed that the two groups respond differently to land-use change: we found less pronounced losses of reptile species richness especially in unburned agricultural habitats, suggesting that reptiles are less susceptible to land-use change than amphibians. Overall, old-growth forest harboured a unique diversity, but some species also thrived in agroforestry systems, especially if these were forest-derived. This highlights the importance of conserving old-growth forests and non-burned land-use types within the agricultural landscape.

LAND USE TYPES AND SOIL CHARACTERISTICTS: A CASE STUDY IN HUONG VINH COMMUNE, HUONG TRA TOWN, THUA THIEN HUE PROVINCE

2017 ◽  
Vol 126 (4B) ◽  
Author(s):  
Trần Thanh Đức
Keyword(s):  
Land Use ◽  
Sweet Potato ◽  
Soil Analysis ◽  
Soil Characteristics ◽  
Low Ph ◽  
Clay Loam ◽  
Total N ◽  
Land Use Types ◽  
Total P

This research carried out in Huong Vinh commune, Huong Tra town, Thua Thien Hue province aimed to identify types of land use and soil characteristics. Results showed that five crops are found in Huong Vinh commune including rice, peanut, sweet potato, cassava and vegetable. There are two major soil orders with four soil suborders classified by FAO in Huong Vinh commune including Fluvisols (Dystric Fluvisols<em>, </em>Gleyic Fluvisols and Cambic Fluvisols) and Arenosols (Haplic Arenosols). The results from soil analysis showed that three soil suborders including Dystric Fluvisols<em>, </em>Gleyic Fluvisols and Cambic Fluvisols belonging to Fluvisols were clay loam in texture, low pH, low in OC, total N, total P<sub>2</sub>O<sub>5</sub> and total K<sub>2</sub>O. Meanwhile, the Haplic Arenosols was loamy sand in texture, poor capacity to hold OC, total N, total P<sub>2</sub>O<sub>5</sub> and total K<sub>2</sub>O

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