Ecology of testate amoebae in an Amazonian peatland and development of a transfer function for palaeohydrological reconstruction

The Effects of Vegetation and the Environment on Testate Amoeba Assemblages in Sphagnum Peatlands in the Northern Caucasus Mountains

Understanding the interactions among the functional groups of living organisms within ecosystems is a main challenge in ecology. This question is particularly important in relation to the interactions between the above- and below-ground components of terrestrial ecosystems. We investigated the effects of macro- (geographic position and mire size) and micro-environmental (pH, water table depth, water mineralization and temperature) characteristics and vegetation composition (both vascular plants and bryophytes) on the species structure of testate amoeba assemblages in eight Sphagnum-dominated mires across the Northern Caucasus Mountains (Russia). In total, 97 testate amoeba species from 34 genera were identified. A multiple factor analysis indicated the strongest relationships between the species structure of the testate amoeba assemblages and the local vegetation, especially bryophytes, whereas the interaction with the micro-environmental characteristics was the weakest. Among the micro-environmental data, the strongest effects on the species composition of all the assemblages were detected for the pH followed by the water table depth and water temperature. The variance partitioning of the species structure of the testate amoeba assemblages in response to the abiotic and biotic data indicated that most of the variance was related to the bryophyte and vascular plant assemblages, whereas the contribution of the environmental data was lower. Moreover, most of the effects were highly related to each other, so that the proportion of the jointly explained variation was high, whereas the individual effects were much lower.

Tropical Peatland Hydrology Simulated With a Global Land Surface Model

Tropical peatlands are among the most carbon-dense ecosystems on Earth, and their water storage dynamics strongly control these carbon stocks. The hydrological functioning of tropical peatlands differs from that of northern peatlands, which has not yet been accounted for in global land surface models (LSMs). Here, we integrated tropical peat-specific hydrology modules into a global LSM for the first time, by utilizing the peatland-specific model structure adaptation (PEATCLSM) of the NASA Catchment Land Surface Model (CLSM). We developed literature-based parameter sets for natural (PEATCLSM_Trop,Nat) and drained (PEATCLSM_Trop,Drain) tropical peatlands. Simulations with PEATCLSM_Trop,Nat were compared against those with the default CLSM version and the northern version of PEATCLSM (PEATCLSM_North,Nat) with tropical vegetation input. All simulations were forced with global meteorological reanalysis input data for the major tropical peatland regions in Central and South America, the Congo Basin, and Southeast Asia. The evaluation against a unique and extensive data set of in situ water level and eddy covariance-derived evapotranspiration showed an overall improvement in bias and correlation compared to the default CLSM version. Over Southeast Asia, an additional simulation with PEATCLSM_Trop,Drain was run to address the large fraction of drained tropical peatlands in this region. PEATCLSM_Trop,Drain outperformed CLSM, PEATCLSM_North,Nat, and PEATCLSM_Trop,Nat over drained sites. Despite the overall improvements of PEATCLSM_Trop,Nat over CLSM, there are strong differences in performance between the three study regions. We attribute these performance differences to regional differences in accuracy of meteorological forcing data, and differences in peatland hydrologic response that are not yet captured by our model.

Testate amoebae: a review on their multiple uses as bioindicators

Testate amoebae (TA) are unicellular protozoans enclosed in a test capable of indicating a wide variety of environmental conditions. Among others, characteristics such as short life cycle, great sensitivity and worldwide distribution makes them adequate bioindicators. As a complement to physical and chemical measurements, biomonitoring can be a cheaper and fastest way of environmental monitoring. This research sought to evaluate the extent of TA use in biomonitoring and the responses given by them to environmental features. The research was conducted in Scielo, Science Direct, Online Library, Google Scholar and Capes Journal Portal and yielded 211 papers. TA bioindication is able to provide information on metal, trace element and atmospheric pollution, and to point out different trophic states, pH, and evidence on characteristics of hydrology. Further, TA can be used in paleoenvironmental reconstruction as they reflect climate, volcanic and even sea level change phenomena. Sometimes, together with other organisms in environmental analysis, they have shown to be an important complement to biomonitoring. Additionally, a functional traits approach has been recently included as a promising tool. Methodological adjustments that have been conducted throughout the years are allowing TA use to be more reliable and precise. This review provides insight on the many possible functions of TA in bioindication studies, highlighting their wide use as bioindicators.

A reassessment of testate amoebae diversity in Tierra del Fuego peatlands: Implications for large scale inferences

Testate amoebae are a diverse group of shelled protists frequently used as model organisms in microbial biogeography. Relatively few species have been reported for the Southern Hemisphere, however, it remains unclear whether this lower diversity is real or an artifact of under-sampling or misidentifications, which would reduce their potential to address macroecological questions. We evaluated testate amoebae diversity from the full range of habitats occurring within two Tierra del Fuego peatlands and compared it with the reported diversity for the area and from the Northern Hemisphere peatlands. We recorded 87 species, of which 69 are new for the region and 45 of them probably new to science and likely to have restricted geographical distributions. Combined with previous studies, the total diversity of testate amoebae only from Tierra del Fuego peatlands now reaches 119, as compared with 183 reported from all Northern Hemisphere peatlands. Our results demonstrate that the number of Gondwanian and Neotropical endemic testate amoeba may be substantially higher than currently known. Previous reports of Holarctic taxa in Tierra del Fuego may result from forcing the identification of morphotypes to the descriptions in the most common literature (force-fitting) South American species into species common in literature from other regions.

First Evidence of Peat Domes in the Congo Basin using LiDAR from a Fixed-Wing Drone

The world’s most extensive tropical peatlands occur in the Cuvette Centrale depression in the Congo Basin, which stores 30.6 petagrams of carbon (95% CI, 6.3–46.8). Improving our understanding of the genesis, development and functioning of these under-studied peatlands requires knowledge of their topography and, in particular, whether the peat surface is domed, as this implies a rain-fed system. Here we use a laser altimeter mounted on an unmanned airborne vehicle (UAV) to measure peat surface elevation along two transects at the edges of a peatland, in the northern Republic of Congo, to centimetre accuracy and compare the results with an analysis of nearby satellite LiDAR data (ICESat and ICESat-2). The LiDAR elevations on both transects show an upward slope from the peatland edge, suggesting a surface elevation peak of around 1.8 m over ~20 km. While modest, this domed shape is consistent with the peatland being rainfed. In-situ peat depth measurements and our LiDAR results indicate that this peatland likely formed at least 10,000 years BP in a large shallow basin ~40 km wide and ~3 m deep.

Tuber borchii Shapes the Ectomycorrhizosphere Microbial Communities of Corylus avellana

In this study, eight-month-old ectomycorrhizae of Tuber borchii with Corylus avellana were synthesized to explore the influence of T. borchii colonization on the soil properties and the microbial communities associated with C. avellana during the early symbiotic stage. The results showed that the bacterial richness and diversity in the ectomycorrhizae were significantly higher than those in the control roots, whereas the fungal diversity was not changed in response to T. borchii colonization. Tuber was the dominant taxon (82.97%) in ectomycorrhizae. Some pathogenic fungi, including Ilyonectria and Podospora, and other competitive mycorrhizal fungi, such as Hymenochaete, had significantly lower abundance in the T. borchii inoculation treatment. It was found that the ectomycorrhizae of C. avellana contained some more abundant bacterial genera (e.g., Rhizobium, Pedomicrobium, Ilumatobacter, Streptomyces, and Geobacillus) and fungal genera (e.g., Trechispora and Humicola) than the control roots. The properties of rhizosphere soils were also changed by T. borchii colonization, like available nitrogen, available phosphorus and exchangeable magnesium, which indicated a feedback effect of mycorrhizal synthesis on soil properties. Overall, this work highlighted the interactions between the symbionts and the microbes present in the host, which shed light on our understanding of the ecological functions of T. borchii and facilitate its commercial cultivation.

Why Do Testate Amoeba Optima Related to Water Table Depth Vary?

This study focusses on the ecology of testate amoeba species in peatlands of the southern taiga of Western Siberia. To estimate the influence of the trophic state of mires on species optima related to water table depth, a separate study of three calibration datasets including ombrotrophic, minerotrophic and the combined habitats was conducted. In the datasets obtained separately from ombrotrophic and minerotrophic mires, the water table depth was the main factor affecting testate amoeba assemblages. However, the trophic state (specifically pH and ash content) was more important factor in the combined dataset, including all of the studied mires. For 36 testate amoeba species, which were found in the ombrotrophic and minerotrophic mire habitats, their species optima, obtained separately in ombrotrophic and minerotrophic datasets, differed significantly from each other. Some of these species preferred minerotrophic conditions, while others preferred ombrotrophic ones. For all species, the trophic state of the mires affected the values of the species optima related to water table depth, as revealed in the form of a threshold effect. In extreme conditions, the species were more sensitive to the trophic status than to the water table depth, and their optimum related to water table depth was distorted. Variation of the optimum was observed in those species that inhabited both ombrotrophic and minerotrophic mires due to the fact that mires with a different trophic status were included in the training sets. The optima did not vary for species inhabiting only ombrotrophic or only minerotrophic mires.

Potential shift from a carbon sink to a source in Amazonian peatlands under a changing climate

Amazonian peatlands store a large amount of soil organic carbon (SOC), and its fate under a future changing climate is unknown. Here, we use a process-based peatland biogeochemistry model to quantify the carbon accumulation for peatland and nonpeatland ecosystems in the Pastaza-Marañon foreland basin (PMFB) in the Peruvian Amazon from 12,000 y before present to AD 2100. Model simulations indicate that warming accelerates peat SOC loss, while increasing precipitation accelerates peat SOC accumulation at millennial time scales. The uncertain parameters and spatial variation of climate are significant sources of uncertainty to modeled peat carbon accumulation. Under warmer and presumably wetter conditions over the 21st century, SOC accumulation rate in the PMFB slows down to 7.9 (4.3-12.2) g⋅C⋅m-2⋅y-1 from the current rate of 16.1 (9.1-23.7) g⋅C⋅m-2⋅y-1, and the region may turn into a carbon source to the atmosphere at -53.3 (-66.8 to -41.2) g⋅C⋅m-2⋅y-1 (negative indicates source), depending on the level of warming. Peatland ecosystems show a higher vulnerability than nonpeatland ecosystems, as indicated by the ratio of their soil carbon density changes (ranging from 3.9 to 5.8). This is primarily due to larger peatlands carbon stocks and more dramatic responses of their aerobic and anaerobic decompositions in comparison with nonpeatland ecosystems under future climate conditions. Peatland and nonpeatland soils in the PMFB may lose up to 0.4 (0.32-0.52) Pg⋅C by AD 2100 with the largest loss from palm swamp. The carbon-dense Amazonian peatland may switch from a current carbon sink into a source in the 21st century.

Light variability and mixotrophy: Responses of testate amoeba communities and shell δ13C values to a peatland shading experiment

Paleoecological records suggest that growing season length and/or cloudiness may affect peatland carbon accumulation and testate amoeba-based environmental reconstructions, highlighting a need to understand how light intensity affects microbial communities. We shaded plots on two peatlands for two years to examine effects on testate amoeba communities, the relative abundance of mixotrophic and heterotrophic testate amoebae, transfer-function performance, and δ¹³C values of two species of mixotrophic testate amoebae. Surprisingly, relative abundance of mixotrophic species increased in shade, although compositional changes did not affect transfer-function performance. Shading did not affect δ¹³C values of Hyalosphenia papilio and Heleopera sphagni, which ranged from -23.5 to -19.6‰ and -23.2 to -19.2‰, respectively. These δ¹³C values were higher than those of potential food sources and lower than literature-derived values for Chlorella, the zoochlorellae inhabiting mixotrophic testate amoebae. δ¹³C values thus suggest that these mixotrophic species obtain some carbon from Chlorella, although coupled dietary and isotope studies are needed to quantify this contribution. More research is needed to assess impacts of light variability on peatland microbial communities; however, carbon sources are recorded by δ¹³C values of testate amoebae, indicating potential for studies of carbon cycling and how mixotrophy varies temporally and spatially.

Evaluation of Morphological Characteristics to Delineate Taxa of the Genus Trigonopyxis (Amoebozoa, Arcellinida)

Morphological features are often the only characteristics suitable for identification of taxa in testate amoebae, especially in ecological and palaeoecological studies. However, whereas the morphology of some species is rather stable it may vary considerably in others. Within the order Arcellinida the genus Trigonopyxis with the type species Trigonopyxis arcula is morphologically highly variable. To identify reliable characteristics for morphology-based taxon delineation we investigated variations in shell size, pseudostome diameter and pseudostome form in T. arcula from three different sites of the Ecuadorian Andes, where these characteristics vary even more than previously described. Further, we investigated if morphological characteristics in Trigonopyxis varied with changes in environmental factors. We studied 951 shells of Trigonopyxis collected along an altitudinal gradient with varying abiotic factors. We established a method for characterization of the pseudostome form, which lead to five different morphotypes. Our results suggest that shell size alone is not an appropriate character for taxon delineation but can be used as an indicator for changes in environmental conditions. In contrast, the pseudostome form might be used for taxon delineation, but likely also varies considerably within taxa. Overall, the study provides an overview of the morphological variability of the genus Trigonopyxis.

Ecosystem state shifts during long-term development of an Amazonian peatland

The most carbon (C)-dense ecosystems of Amazonia are areas characterized by the presence of peatlands. However, Amazonian peatland ecosystems are poorly understood and are threatened by human activities. Here, we present an investigation into long-term ecohydrological controls on C accumulation in an Amazonian peat dome. This site is the oldest peatland yet discovered in Amazonia (peat initiation ca. 8.9 ka BP), and developed in three stages: (i) peat initiated in an abandoned river channel with open water and aquatic plants; (ii) inundated forest swamp; and (iii) raised peat dome (since ca. 3.9 ka BP). Local burning occurred at least three times in the past 4,500 years. Two phases of particularly rapid C accumulation (ca. 6.6-6.1 and ca. 4.9-3.9 ka BP), potentially resulting from increased net primary productivity, were seemingly driven by drier conditions associated with widespread drought events. The association of drought phases with major ecosystem state shifts (open water wetland-forest swamp-peat dome) suggests a potential climatic control on the developmental trajectory of this tropical peatland. A third drought phase centred on ca. 1.8-1.1 ka BP led to markedly reduced C accumulation and potentially a hiatus during the peat dome stage. Our results suggest that future droughts may lead to phases of rapid C accumulation in some inundated tropical peat swamps, although this can lead ultimately to a shift to ombrotrophy and a subsequent return to slower C accumulation. Conversely, in ombrotrophic peat domes, droughts may lead to reduced C accumulation or even net loss of peat. Increased surface wetness at our site in recent decades may reflect a shift towards a wetter climate in western Amazonia. Amazonian peatlands represent important carbon stores and habitats, and are important archives of past climatic and ecological information. They should form key foci for conservation efforts.

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis

BACKGROUND

Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure.

RESULTS

The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors.

CONCLUSIONS

The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

Testate amoeba transfer function performance along localised hydrological gradients

Testate amoeba transfer functions are widely used for reconstruction of palaeo-hydrological regime in peatlands. However, the limitations of this approach have become apparent with increasing attention to validation and assessing sources of uncertainty. This paper investigates effects of peatland type and sampling depth on the performance of a transfer function using an independent test-set from four Sphagnum-dominated sites in European Russia (Penza Region). We focus on transfer function performance along localised hydrological gradients, which is a useful analogue for predictive ability through time. The performance of the transfer function with the independent test-set was generally weaker than for the leave-one-out or bootstrap cross-validations. However, the transfer function was robust for the reconstruction of relative changes in water-table depth, provided the presence of good modern analogues and overlap in water-table depth ranges. When applied to subsurface samples, the performance of the transfer function was reduced due to selective decomposition, the presence of deep-dwelling taxa or vertical transfer of shells. Our results stress the importance of thorough testing of transfer functions, and highlight the role of taphonomic processes in determining results. Further studies of stratification, taxonomy and taphonomy of testate amoebae will be needed to improve the robustness of transfer function output.

First discovery of Holocene cryptotephra in Amazonia

The use of volcanic ash layers for dating and correlation (tephrochronology) is widely applied in the study of past environmental changes. We describe the first cryptotephra (non-visible volcanic ash horizon) to be identified in the Amazon basin, which is tentatively attributed to a source in the Ecuadorian Eastern Cordillera (0-1°S, 78-79°W), some 500-600 km away from our field site in the Peruvian Amazon. Our discovery 1) indicates that the Amazon basin has been subject to volcanic ash fallout during the recent past; 2) highlights the opportunities for using cryptotephras to date palaeoenvironmental records in the Amazon basin and 3) indicates that cryptotephra layers are preserved in a dynamic Amazonian peatland, suggesting that similar layers are likely to be present in other peat sequences that are important for palaeoenvironmental reconstruction. The discovery of cryptotephra in an Amazonian peatland provides a baseline for further investigation of Amazonian tephrochronology and the potential impacts of volcanism on vegetation.

Hydroecology of Amazonian lacustrine Arcellinida (testate amoebae): A case study from Lake Quistococha, Peru

Organic rich sediments were obtained from seven core tops taken in Lake Quistococha, near the city of Iquitos in the Peruvian Amazon. Subsamples from 0 to 4cm depth in each core were analyzed under dissecting light microscopy to carry out the first investigation of Arcellinida (testate lobose amoebae) from a lacustrine environment in this ecologically important region. The fauna was characterized by a low diversity, low abundance community dominated by centropyxids. This fauna is similar to 'stressed' assemblages reported from temperate latitudes, except that test concentrations were two orders of magnitude lower than typical in temperate lakes. Principle arcellinidan stressors in Lake Quistococha likely include the low pH 4 conditions in the lake, and a general lack of suitable minerogenic material to construct tests in the organic rich lake substrate. The low pH conditions are the result of runoff and seepage of water high in dissolved organic carbon from the adjacent similarly low pH 4 terrestrial peatland. The dearth of minerogenic material is the result of the lake being isolated from riverine input for the past ∼2000 years, even during flooding events. Other limiting factors contributing to depressed arcellinidan populations may include nutrient supply, predation pressure, competition, and post-mortem taphonomic factors.

Peatland Microbial Communities as Indicators of the Extreme Atmospheric Dust Deposition

We investigated a peat profile from the Izery Mountains, located within the so-called Black Triangle, the border area of Poland, Czech Republic, and Germany. This peatland suffered from an extreme atmospheric pollution during the last 50 years, which created an exceptional natural experiment to examine the impact of pollution on peatland microbes. Testate amoebae (TA), Centropyxis aerophila and Phryganella acropodia, were distinguished as a proxy of atmospheric pollution caused by extensive brown coal combustion. We recorded a decline of mixotrophic TA and development of agglutinated taxa as a response for the extreme concentration of Al (30 g kg^-1) and Cu (96 mg kg^-1) as well as the extreme amount of fly ash particles determined by scanning electron microscopy (SEM) analysis, which were used by TA for shell construction. Titanium (5.9 %), aluminum (4.7 %), and chromium (4.2 %) significantly explained the highest percentage of the variance in TA data. Elements such as Al, Ti, Cr, Ni, and Cu were highly correlated (r > 0.7, p < 0.01) with pseudostome position/body size ratio and pseudostome position. Changes in the community structure, functional diversity, and mechanisms of shell construction were recognized as the indicators of dust pollution. We strengthen the importance of the TA as the bioindicators of the recent atmospheric pollution.