Forest tree growth is linked to mycorrhizal fungal composition and function across Europe

Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how we monitor marine ecosystems. The time-consuming pre-processing step of active filtration, however, remains a bottleneck. Hence, new approaches omitting active filtration are in great demand. One exciting prospect is to use the filtering power of invertebrates to collect eDNA. While proof-of-concept has been achieved, comparative studies between aquatic and filter feeder eDNA signals are lacking. Here, we investigated the differences among four eDNA sources (water; bivalves; sponges; and ethanol in which filter-feeding organisms were stored) along a vertical transect in Doubtful Sound, New Zealand using three metabarcoding primers (fish (16S); MiFish-E/U). While concurrent SCUBA diver observations validated eDNA results, laboratory trials corroborated in-field bivalve eDNA detection results. Combined, eDNA sources detected 59 vertebrates, while divers observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was detected in ethanol, although only a reduced number of species were detected. Bivalves failed to reliably detect eDNA in both field and mesocosm experiments. While additional research into filter feeder eDNA accumulation efficiency is essential, our results provide strong evidence for the potential of incorporating sponges into eDNA surveys.

Mitigation of CyanoHABs Using Phoslock® to Reduce Water Column Phosphorus and Nutrient Release from Sediment

Cyanobacterial blooms can be stimulated by excessive phosphorus (P) input, especially when diazotrophs are the dominant species. A series of mesocosm experiments were conducted in a lake dominated by a cyanobacteria bloom to study the effects of Phoslock®, a phosphorus adsorbent. The results showed that the addition of Phoslock® lowered the soluble reactive phosphate (SRP) concentrations in water due to efficient adsorption and mitigated the blooms. Once settled on the sediments, Phoslock® serves as a barrier to reduce P diffusion from sediments into the overlying waters. In short-term (1 day) incubation experiments, Phoslock® diminished or reversed SRP effluxes from bottom sediments. At the same time, the upward movement of the oxic–anoxic interface through the sediment column slightly enhanced NH4+ release and depressed N2 release, suggesting the inhibition of nitrification and denitrification. In a long-term (28 days) experiment, Phoslock® hindered the P release, reduced the cyanobacterial abundance, and alleviated the bloom-driven enhancements in the pH and oxygen. These results suggest that, through suppression of internal nutrient effluxes, Phoslock® can be used as an effective control technology to reduce cyanobacteria blooms common to many freshwater systems.

Effect of Extreme Heatwaves on the Mortality and Cellular Immune Responses of Purplish Bifurcate Mussel Mytilisepta virgata (Wiegmann, 1837) (=Septifer virgatus) in Indoor Mesocosm Experiments

In the rocky intertidal environment, the frequency and duration of heatwaves have increased over the last decade, possibly due to global climate change. Heatwaves often result in lethal or sub-lethal disturbances in benthic animals by changing their metabolic activities. In this study, we investigated the impacts of extreme heatwave stress on the hemocyte functions of Mytilisepta virgata and subsequent mortality to gain a better understanding of the potential causes and consequences of mass mortality events in this mussel during summer. We discriminated three types of hemocytes in the hemolymph, granulocytes, hyalinocytes, and blast-like cells, using flow cytometry and revealed that granulocytes were the major hemocyte involved in cellular defensive activities, such as phagocytosis and reactive oxygen species (ROS) production. For the experiment, mussels were exposed to a 40°C air temperature for 12 h per day over 5 days under laboratory conditions as a simulated semi-diurnal tidal cycle. Mortality began to occur within 3 days after beginning the experiment, and all mussels had died by the end of the experiment. Flow cytometry indicated that the mussels exposed to high air temperatures produced significantly more ROS than did the control mussels within 2 days after the onset of the experiment, which may have caused oxidative stress. Such high levels of ROS in the hemolymph increased DNA damage in hemocytes after 3 days of exposure and decreased the phagocytosis of hemocytes 4 days after the experiment began. The observed mortality and decline in immune capacity suggested that an extreme heat event occurring in the rocky intertidal ecosystem during summer could exert sublethal to lethal impacts on macrobenthic animals.

Thresholds of acidification impacts on macroinvertebrates adapted to seasonally acidified tropical streams: potential responses to extreme drought-driven pH declines

Background Drought-driven acidification events of increasing frequency and severity are expected as a consequence of climate change, and these events may expose macroinvertebrate taxa to increased acidification beyond their tolerance levels. Recent work in lowland Costa Rica has shown that poorly-buffered tropical streams exhibit natural seasonal variation in pH, with extremely low levels (<4.5) after extreme dry seasons). Our goal was to determine the threshold of pH effects on survival of three tropical stream macroinvertebrate taxa. Methods We conducted laboratory mesocosm experiments to determine acidification effects (using diluted HCl) on three focal macroinvertebrate taxa collected from a poorly-buffered stream at La Selva Biological Station: (1) mayfly naiads (Ephemeroptera: Leptophlebiidae: Traverella holzenthali), (2) adult shrimp (Decapoda: Palaemonidae: Macrobrachium olfersii), and (3) larval midges (Diptera: Chironomidae). We also compared the effect of pH on survival and growth rates of larval midges from a poorly-buffered (pH 4.3–6.9) vs. a naturally well-buffered (pH 5.1–6.9) stream. Results/Discussion Mayfly and shrimp survival decreased between pH 4.0 and 3.5, overlapping with the range of lowest pH levels (3.6–4.0) recorded during a previous extreme El Niño Southern Oscillation event in 1998 and suggesting that increasingly extreme acidification events induced by climate change may negatively affect their survival. In contrast, survival of larval midges was unaffected by pH regimes at/above 3.5, indicating tolerance to pH levels experienced in poorly-buffered stream during seasonal acidification, which has presumably occurred over millennia. These findings highlight the potential importance of historical pH regimes in structuring macroinvertebrate communities. These results are relevant not only to lowland Neotropical streams, but also signal the need for further research in lotic ecosystems worldwide where drought-driven pH declines have been documented or are probable in the future.

Can Alkyl Quaternary Ammonium Cations Substitute H2O2 in Controlling Cyanobacterial Blooms—Laboratory and Mesocosm Studies

Mitigation of harmful cyanobacterial blooms that constitute a serious threat to water quality, particularly in eutrophic water, such as in aquaculture, is essential. Thus, in this study, we tested the efficacy of selected cyanocides towards bloom control in laboratory and outdoor mesocosm experiments. Specifically, we focused on the applicability of a group of cationic disinfectants, alkyltrimethyl ammonium (ATMA) compounds and H2O2. The biocidal effect of four ATMA cations with different alkyl chain lengths was evaluated ex situ using Microcystis colonies collected from a fish pond. The most effective compound, octadecyl trimethyl ammonium (ODTMA), was further evaluated for its selectivity towards 24 cyanobacteria and eukaryotic algae species, including Cyanobacteria, Chlorophyta, Bacillariophyta, Euglenozoa and Cryptophyta. The results indicated selective inhibition of cyanobacteria by ODTMA-Br (C18) on both Chroccocales and Nostocales, but a minor effect on Chlorophytes and Bacillariophytes. The efficacy of ODTMA-Br (C18) (6.4 μM) in mitigating the Microcystis population was compared with that of a single low dose of H2O2 treatments (117.6 μM). ODTMA-Br (C18) suppressed the regrowth of Microcystis for a longer duration than did H2O2. The results suggested that ODTMA-Br (C18) may be used as an effective cyanocide and that it is worth further evaluating this group of cationic compounds as a treatment to mitigate cyanobacterial blooms in aquaculture.

Phenotypic Variation Through Ontogeny: Thyroid Axis Disruption During Larval Development in the Frog Pleurodema borellii

Studies of the effects of thyroid hormones on larval development in the frog Xenopus spp. have provided baseline information to identify developmental constraints and elucidate genetic and hormonal mechanisms driving development, growth, and life history transitions. However, this knowledge requires data based on other anurans to complete a comprehensive approach to the understanding of larval developmental diversity and phenotypic variation through ontogeny. Mesocosm experiments provide realistic data about environmental conditions and timing; this information is useful to describe anuran larval development and/or analyze endocrine disruption. In this study, mesocosm experiments of the larval development of the frog Pleurodema borellii were conducted to explore the consequences of thyroid axis disruption; the sensitivity of tadpoles to the methimazole (2.66 mg/l) and thyroxine (T4) (1.66 μg/l) was compared. These concentrations were selected based on previous studies in Pleurodema borellii. We test the effects of methimazole and thyroxine on development in early exposure (from beginning of larval development) and late exposure, 18 days after hatching, with doses administered every 48 h. Tadpoles were evaluated 31 days after hatching. Methimazole caused moderate hypertrophy of the thyroid gland, alteration in the growth rates, differentiation without inhibition of development, and an increase of developmental variability. Thyroxine produced slight atrophy of the thyroid gland, accelerated growth rates and differentiation, and minor developmental variability. In tadpoles at stages previous to metamorphose, skull development (differentiation of olfactory capsules, appearance of dermal bones, and cartilage remodeling) seemed to be unaltered by the disruptors. Moreover, similar abnormal morphogenesis converged in specimens under methimazole and thyroxine exposures. Abnormalities occurred in pelvic and pectoral girdles, and vent tube, and could have been originated at the time of differentiation of musculoskeletal tissues of girdles. Our results indicate that premetamorphic stages (Gosner Stages 25–35) are sensitive to minimal thyroid axis disruption, which produces changes in developmental rates; these stages would also be critical for appendicular musculoskeletal morphogenesis to achieve the optimal condition to start metamorphosis.

KGML-ag: A Modeling Framework of Knowledge-Guided Machine Learning to Simulate Agroecosystems: A Case Study of Estimating N₂O Emission using Data from Mesocosm Experiments

Agricultural nitrous oxide (N2O) emission accounts for a non-trivial fraction of global greenhouse gases (GHGs) budget. To date, estimating N2O fluxes from cropland remains a challenging task because the related microbial processes (e.g., nitrification and denitrification) are controlled by complex interactions among climate, soil, plant and human activities. Existing approaches such as process-based (PB) models have well-known limitations due to insufficient representations of the processes or constraints of model parameters, and to leverage recent advances in machine learning (ML) new method is needed to unlock the “black box” to overcome its limitations due to low interpretability, out-of-sample failure and massive data demand. In this study, we developed a first of its kind knowledge-guided machine learning model for agroecosystems (KGML-ag), by incorporating biogeophysical/chemical domain knowledge from an advanced PB model, ecosys, and tested it by simulating daily N2O fluxes with real observed data from mesocosm experiments. The Gated Recurrent Unit (GRU) was used as the basis to build the model structure. To optimize the model performance, we have investigated a range of ideas, including: 1) Using initials of intermediate variables (IMVs) instead of time series as model input to reduce data demand; 2) Building hierarchical structures to explicitly estimate IMVs for further N2O prediction; 3) Using multitask learning to balance the simultaneous training on multiple variables; and 4) Pretraining with millions of synthetic data generated from ecosys and fine tuning with mesocosm observations. Six other pure ML models were developed using the same mesocosm data to serve as the benchmark for the KGML-ag model. Results show that KGML-ag did an excellent job in reproducing the mesocosm N2O fluxes (overall r2 = 0.81, and RMSE = 3.6 mg N m−2 day−1 from cross-validation). Importantly KGML-ag always outperforms the PB model and ML models in predicting N2O fluxes, especially for complex temporal dynamics and emission peaks. Besides, KGML-ag goes beyond the pure ML models by providing more interpretable predictions as well as pinpointing desired new knowledge and data to further empower the current KGML-ag. We believe the KGML-ag development in this study will stimulate a new body of research on interpretable ML for biogeochemistry and other related geoscience processes.