scholarly journals Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding

2021 ◽  
Author(s):  
Camila Duarte Ritter ◽  
Dominik Forster ◽  
Josue A. R. Azevedo ◽  
Alexandre Antonelli ◽  
R. Henrik Nilsson ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
High Turnover ◽  
Saprotrophic Fungi ◽  
White Sand ◽  
Network Analyses ◽  
Dna Metabarcoding ◽  
Network Properties ◽  
Mineral Soils ◽  
Seasonally Flooded ◽  
Abiotic Interactions

AbstractSpecies may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (várzeas) or by unfertile black waters (igapós), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian microorganism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region.

scholarly journals Assessing biotic and abiotic interactions of micro-organisms in Amazonia through co-occurrence networks and DNA metabarcoding

2021 ◽  
Author(s):  
Camila DUARTE Duarte Ritter ◽  
Dominik Forster ◽  
Josue A. R. Azevedo ◽  
Alexandre Antonelli ◽  
R. Henrik Nilsson ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
High Turnover ◽  
Saprotrophic Fungi ◽  
White Sand ◽  
Network Analyses ◽  
Dna Metabarcoding ◽  
Mineral Soils ◽  
Seasonally Flooded ◽  
Micro Organisms ◽  
Abiotic Interactions

Abstract Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (várzeas) or by unfertile black waters (igapós), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian micro-organism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region.

scholarly journals Distance from the Forest Edge Influences Soil Fungal Communities Colonizing a Reclaimed Soil Borrow Site in Boreal Mixedwood Forest

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 427 ◽  
Author(s):  
Tod Ramsfield ◽  
Philip-Edouard Shay ◽  
Tony Trofymow ◽  
Colin Myrholm ◽  
Bradley Tomm ◽  
...  
Keyword(s):  
Ectomycorrhizal Fungi ◽  
Arbuscular Mycorrhizae ◽  
Plant Pathogens ◽  
Forest Edge ◽  
Natural Forest ◽  
Fungal Communities ◽  
Saprotrophic Fungi ◽  
Reclaimed Soil ◽  
Undisturbed Forest ◽  
Mineral Soils

Soil fungi are important components of boreal forest ecosystems; for example, saprotrophic fungi regulate nutrient cycling, and mycorrhizal species facilitate nutrient uptake by plants. This study aimed to assess soil fungal communities in a reclaimed area and an adjacent natural mixedwood forest and to identify the distribution of taxa available for seedling colonization. Soil fungal microbiomes were assessed along three transects (from 10 m inside the interior of the undisturbed forest to 40 m inside the reclaimed area) and in the roots of small aspen within the natural forest. Using high-throughput deoxyribonucleic acid (DNA) sequencing of internal transcribed spacer amplicons, a total of 2796 unique fungal taxa were detected across fine roots, forest floor, and mineral soils collected along the transects, whereas 166 taxa were detected in the aspen roots from the natural forest. Within the interior of the forest, ectomycorrhizal fungi were more common, whereas in the reclaimed areas, arbuscular mycorrhizae and saprophytes were more common. This survey showed that natural areas of adjacent undisturbed forest can act as a source of ectomycorrhizal fungi for dispersal into reclaimed areas. Notably, soil fungal taxa colonizing the root systems of small aspen included species that are specifically associated with soils from the undisturbed forest (primarily ectomycorrhizae) or the reclaimed clearing (saprotrophs and plant pathogens).

What is the avifauna of Amazonian white-sand vegetation?

2015 ◽  
Vol 26 (2) ◽  
pp. 192-204 ◽  
Author(s):  
SÉRGIO HENRIQUE BORGES ◽  
CINTIA CORNELIUS ◽  
CAMILA RIBAS ◽  
RICARDO ALMEIDA ◽  
EDSON GUILHERME ◽  
...  
Keyword(s):  
Environmental History ◽  
Indicator Species ◽  
Amazon Basin ◽  
Vegetation Type ◽  
Bird Species ◽  
White Sand ◽  
Flooded Forests ◽  
Areas Of Endemism ◽  
History Of ◽  
Seasonally Flooded

SummaryWhite-sand vegetation (WSV) is a rare vegetation type in the Amazon basin that grows in nutrient impoverished sandy soils that occur as patches of variable size. Associated with this vegetation is bird assemblage that has not yet been fully characterized. Based on published species inventories and our own field data we compile a checklist of bird species recorded in WSV. In addition, we compared the avifauna of WSV with that found in savanna patches, another type of Amazonian open vegetation. WSV hosted a distinctive avifauna including endemic and threatened species. The number of bird species was lower in WSV compared to nearby terra firme forests, seasonally flooded forests and Amazonian savannas. Despite its low diversity, the avifauna of WSV has a distinctive species composition and makes a significant contribution to Amazonian beta diversity. At least 35 bird species can be considered as indicator species for this environment. Previously identified areas of endemism within the Amazon basin house at least one WSV indicator bird including cases of congeneric species with allopatric distributions. Seven of the WSV indicator species (20% of this avifauna) are in an IUCN threatened category, with one species Polioptila clementsi considered Critically Endangered. Their isolated distribution, small area occupied, and fragility to human-driven disturbances makes WSV one of the most threatened vegetation types in the Amazon basin. The study of WSV avifauna contributes to a better understanding of mechanisms that generate and maintain species diversity as well as of the environmental history of the most biologically diverse biome of the planet.

scholarly journals Landscape-level DNA metabarcoding study in the Pannonian forests reveals differential effects of slope aspect on taxonomic and functional groups of fungi

2018 ◽  
Author(s):  
József Geml
Keyword(s):  
Functional Groups ◽  
Community Composition ◽  
Fungal Community ◽  
Environmental Conditions ◽  
Community Dynamics ◽  
Fungal Communities ◽  
Slope Aspect ◽  
Fungal Community Composition ◽  
Dna Metabarcoding ◽  
Landscape Level

AbstractIn temperate regions, slope aspect is one of the most influential drivers of environmental conditions at landscape level. The effect of aspect on vegetation has been well studied, but virtually nothing is known about how fungal communities are shaped by aspect-driven environmental conditions. I carried out DNA metabarcoding of fungi from soil samples taken in a selected study area of Pannonian forests to compare richness and community composition of taxonomic and functional groups of fungi between slopes of predominantly southerly vs. northerly aspect and to assess the influence of selected environmental variables on fungal community composition. The deep sequence data presented here (i.e. 980 766 quality-filtered sequences) indicate that both niche (environmental filtering) and neutral (stochastic) processes shape fungal community composition at landscape level. Fungal community composition correlated strongly with aspect, with many fungi showing preference for either south-facing or north-facing slopes. Several taxonomic and functional groups showed significant differences in richness between north-and south-facing slopes and strong compositional differences were observed in all functional groups. The effect of aspect on fungal communities likely is mediated through contrasting mesoclimatic conditions, that in turn influence edaphic processes as well as vegetation. Finally, the data presented here provide an unprecedented insight into the diversity and landscape-level community dynamics of fungi in the Pannonian forests.

scholarly journals Professional advice for primary healthcare workers in Ethiopia: a social network analysis

2020 ◽  
Author(s):  
Kate Sabot ◽  
Karl Blanchet ◽  
Della Berhanu ◽  
Neil Spicer ◽  
Joanna Schellenberg
Keyword(s):  
Primary Healthcare ◽  
Healthcare Workers ◽  
Qualitative Interviews ◽  
Health Centre ◽  
Density Ratio ◽  
Newborn Care ◽  
Professional Advice ◽  
Network Analyses ◽  
Advice Networks ◽  
Network Properties

Abstract Background In an era of increasingly competitive funding, governments and donors will be looking for creative ways to extend and maximise resources. One such means can include building upon professional advice networks to more efficiently introduce, scale up, or change programmes and healthcare provider practices. This cross-sectional, mixed-methods, observational study compared professional advice networks of healthcare workers in eight primary healthcare units across four regions of Ethiopia. Primary healthcare units include a health centre and typically five satellite health posts.Methods 160 staff at eight primary healthcare units were interviewed using a structured tool. Quantitative data captured the frequency of healthcare worker advice seeking and giving on providing antenatal, childbirth, postnatal and newborn care. Network and actor-level metrics were calculated including density (ratio of ties between actors to all possible ties), centrality (number of ties incident to an actor), distance (average number of steps between actors) and size (number of actors within the network). Following quantitative network analyses, 20 qualitative interviews were conducted with network study participants from four primary healthcare units. Qualitative interviews aimed to interpret and explain network properties observed. Data were entered, analysed or visualised using Excel 6.0, UCINET 6.0, Netdraw, Adobe InDesign and MaxQDA10 software packages.Results The following average network level metrics were observed: density .26 (SD.11), degree centrality .45 (SD.08), distance 1.94 (SD.26), number of ties 95.63 (SD 35.46), size of network 20.25 (SD 3.65). Advice networks for antenatal or maternity care were more utilised than advice networks for post-natal or newborn care. Advice networks were typically limited to primary healthcare unit staff, but not necessarily to supervisors. In seeking advice, a colleague’s level of training and knowledge were valued over experience. Advice exchange primarily took place in person or over the phone rather than over email or online fora. There were few barriers to seeking advice.Conclusion Informal, inter-and intra-cadre advice networks existed. Fellow primary healthcare unit staff were preferred, particularly midwives, but networks were not limited to the primary healthcare unit. Additional research is needed to associate network properties with outcomes and pilot network interventions with central actors.

scholarly journals Shifting mineral and redox controls on carbon cycling in seasonally flooded mineral soils

2019 ◽  
Vol 16 (13) ◽  
pp. 2573-2589 ◽  
Author(s):  
Rachelle E. LaCroix ◽  
Malak M. Tfaily ◽  
Menli McCreight ◽  
Morris E. Jones ◽  
Lesley Spokas ◽  
...  
Keyword(s):  
Climate Change ◽  
Redox Potential ◽  
Organic Compounds ◽  
Root Biomass ◽  
Wetland Soils ◽  
Co2 Efflux ◽  
Seasonal Flooding ◽  
Upland Soils ◽  
Mineral Soils ◽  
Seasonally Flooded

Abstract. Although wetland soils represent a relatively small portion of the terrestrial landscape, they account for an estimated 20 %–30 % of the global soil carbon (C) reservoir. C stored in wetland soils that experience seasonal flooding is likely the most vulnerable to increased severity and duration of droughts in response to climate change. Redox conditions, plant root dynamics, and the abundance of protective mineral phases are well-established controls on soil C persistence, but their relative influence in seasonally flooded mineral soils is largely unknown. To address this knowledge gap, we assessed the relative importance of environmental (temperature, soil moisture, and redox potential) and biogeochemical (mineral composition and root biomass) factors in controlling CO2 efflux, C quantity, and organic matter composition along replicated upland–lowland transitions in seasonally flooded mineral soils. Specifically, we contrasted mineral soils under temperature deciduous forests in lowland positions that undergo seasonal flooding with adjacent upland soils that do not, considering both surface (A) and subsurface (B and C) horizons. We found the lowland soils had lower total annual CO2 efflux than the upland soils, with monthly CO2 efflux in lowlands most strongly correlated with redox potential (Eh). Lower CO2 efflux as compared to the uplands corresponded to greater C content and abundance of lignin-rich, higher-molecular-weight, chemically reduced organic compounds in the lowland surface soils (A horizons). In contrast, subsurface soils in the lowland position (Cg horizons) showed lower C content than the upland positions (C horizons), coinciding with lower abundance of root biomass and oxalate-extractable Fe (Feo, a proxy for protective Fe phases). Our linear mixed-effects model showed that Feo served as the strongest measured predictor of C content in upland soils, yet Feo had no predictive power in lowland soils. Instead, our model showed that Eh and oxalate-extractable Al (Alo, a proxy of protective Al phases) became significantly stronger predictors in the lowland soils. Combined, our results suggest that low redox potentials are the primary cause for C accumulation in seasonally flooded surface soils, likely due to selective preservation of organic compounds under anaerobic conditions. In seasonally flooded subsurface soils, however, C accumulation is limited due to lower C inputs through root biomass and the removal of reactive Fe phases under reducing conditions. Our findings demonstrate that C accrual in seasonally flooded mineral soil is primarily due to low redox potential in the surface soil and that the lack of protective metal phases leaves these C stocks highly vulnerable to climate change.

scholarly journals White-Sand Savannas Expand at the Core of the Amazon After Forest Wildfires

Ecosystems ◽  
2021 ◽  
Author(s):  
Bernardo M. Flores ◽  
Milena Holmgren
Keyword(s):  
Tree Species ◽  
Amazon Basin ◽  
Forest Tree ◽  
Landsat Images ◽  
Tree Species Composition ◽  
White Sand ◽  
The Core ◽  
Ecosystem Shift ◽  
Seasonally Flooded ◽  
Satellite Analysis

AbstractAcross the tropics, climate change is increasing the frequency and severity of wildfires, exposing tropical forests to the risk of shifting into an open vegetation state. A recent satellite analysis of the Amazon basin suggests this might happen first in floodplains where forests are particularly fragile. We studied floodplain landscapes of the middle Rio Negro, covering ~ 4100 km2 at the Central Amazon region, where forest ecosystems are dominant. We used Landsat images to map 40 years of wildfire history and test the hypothesis that repeatedly burnt forests fail to regenerate and can be replaced by white-sand savanna ecosystems. In the field, using a chronosequence of ‘time after the first fire’, we assessed changes in tree species composition, herbaceous cover and topsoil properties. Here we show that when these forests are repeatedly disturbed by wildfires, their soil gradually loses clay and nutrients and becomes increasingly sandy. In synchrony, native herbaceous cover expands, forest tree species disappear and white-sand savanna tree species become dominant. This drastic ecosystem shift happened within 40 years, likely accelerated by topsoil erosion. When recurrent fires maintain floodplain forests in an open vegetation state, topsoil erosion intensifies, transforming clay-rich soils into white-sand soils that may favour savanna tree species. Our findings reveal that white-sand savannas may expand through seasonally flooded ecosystems at the core of the Amazon, facilitated by wildfires.

scholarly journals Expanding forests in alpine regions: space-for-time indicates a corresponding shift in belowground fungal communities

2021 ◽  
Author(s):  
Lea-Rebekka Tonjer ◽  
Ella Thoen ◽  
Luis Morgado ◽  
Synnøve Smebye Botnen ◽  
Sunil Mundra ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
C Sequestration ◽  
Soil Biota ◽  
Mountain Birch ◽  
Saprotrophic Fungi ◽  
Strong Shift ◽  
Alpine Regions ◽  
Dna Metabarcoding ◽  
Compositional Changes ◽  
Forest Line

Climate change causes upward shift of forest lines worldwide, with consequences on soil biota and carbon (C). Using a space-for-time approach, we analyse compositional changes in the soil biota across the forest line ecotone, an important transition zone between different ecosystems. We collected soil samples along transects stretching from subalpine mountain birch forests to low-alpine vegetation. Soil fungi and micro-eukaryotes were surveyed using DNA metabarcoding of the 18S and ITS2 markers, while ergosterol was used to quantify fungal biomass. We observed a strong shift in the soil biota across the forest line ecotone: Below the forest line, there were higher proportions of basidiomycetes and mucoromycetes, including ectomycorrhizal and saprotrophic fungi. Above, we observed relatively more root-associated ascomycetes, including Archaeorhizomycetes, ericoid mycorrhizal fungi and dark septate endophytes. Ergosterol and percentage C content in soil strongly and positively correlated with the abundance of root-associated ascomycetes. The predominance of ectomycorrhizal and saprotrophic fungi below the forest line likely promote high C turnover, while root-associated ascomycetes above the forest line may enhance C sequestration. With further rise in forest lines, there will be a corresponding shift in the belowground biota linked to C sequestration processes.

scholarly journals Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties

2020 ◽  
Vol 4 ◽  
Author(s):  
Lina A. Clasen ◽  
Andrew P. Detheridge ◽  
John Scullion ◽  
Gareth W. Griffith
Keyword(s):  
Freeze Drying ◽  
Storage Conditions ◽  
Third Parties ◽  
Stochastic Variation ◽  
Saprotrophic Fungi ◽  
Soil Stabilisation ◽  
Dna Metabarcoding ◽  
Biotrophic Fungi ◽  
Storage Methods ◽  
Initial Freezing

Storage of soil samples prior to metagenomic analysis presents a problem. If field sites are remote or if samples are collected by third parties, transport to analytical laboratories may take several days or even weeks. The bulk of such samples and requirement for later homogenisation precludes the convenient use of a stabilisation buffer, so samples are usually cooled or frozen during transit. There has been limited testing of the most appropriate storage methods for later study of soil organisms by eDNA approaches. Here we tested a range of storage methods on two contrasting soils, comparing these methods to the control of freezing at -80 °C, followed by freeze-drying. To our knowledge, this is the first study to examine the effect of storage conditions on eukaryote DNA in soil, including both viable organisms (fungi) and DNA contained within dying/dead tissues (plants). For fungi, the best storage regimes (closest to the control) were storage at 4 °C (for up to 14 d) or active air-drying at room temperature. The worst treatments involved initial freezing, followed by thawing which led to significant later spoilage. The key spoilage organisms were identified as Metarhizium carneum and Mortierella spp., with a general increase in saprotrophic fungi and reduced abundances of mycorrhizal/biotrophic fungi. Plant data showed a similar pattern, but with greater variability in community structure, especially in the freeze-thaw treatments, probably due to stochastic variation in substrates for fungal decomposition, algal proliferation and some seed germination. In the absence of freeze drying facilities, samples should be shipped refrigerated, but not frozen if there is any risk of thawing.

scholarly journals Evaluation of biodiversity in estuaries using environmental DNA metabarcoding

2020 ◽  
Author(s):  
Hyojin Ahn ◽  
Manabu Kume ◽  
Yuki Terashima ◽  
Feng Ye ◽  
Satoshi Kameyama ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Conditions ◽  
Environmental Dna ◽  
Aquatic Biodiversity ◽  
Non Invasive ◽  
Dna Metabarcoding ◽  
And Migration ◽  
Low Degrees ◽  
River Mouths ◽  
Rare Fishes

AbstractBiodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river, suggesting the potential of eDNA for non-invasive assessment of aquatic biodiversity.

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