Deciphering soil nematode‐bacteria‐fungi community composition and functional dynamics in coffee agroecosystems under conventional and sustainable management practices in Costa Rica

Understanding the interactions between soil bacteria, fungi, and nematodes in coffee agroecosystems is crucial for optimiz- ing sustainable agriculture. This study investigated the composition and functional dynamics of these communities under conventional and sustainable management systems. Soil samples were collected from three major coffee-growing regions in Costa Rica, representing different agricultural regimes. Nematode community was analyzed using optical microscopy, while microbial communities were analyzed using high-throughput sequencing. In both cases, bioinformatic tools were used for functional prediction based on taxonomy.. Herbivorous nematodes dominated both systems, while bacterivores (Rhabditidae, Cephalobidae) and fungivores (Aphelenchoidae) were significantly more abundant in soils subject to sustain- able practice (p < 0.05). Nematode maturity indices and food web diagnostics showed no significant differences between systems, even though metabolic footprints related to organic matter decomposition varied (p<0.05). Bacterial communi- ties were dominated by the phyla Proteobacteria, Acidobacteria, and Chloroflexi, while the fungal community was largely composed of Ascomycota (53.21% in both systems). The fungal genus Mortierella was particularly prevalent. Soil pH, along with Ca, Mg, K, and extractable acidity, influenced community composition. Functional profiles revealed higher gene abundances linked to nutrient and energy cycling in sustainable systems, particularly phosphorus and sulfur metabolism. Saprotroph-symbiotroph fungi were more common in sustainable soils, while pathotrophic fungi dominated conventional systems. This is the first comprehensive analysis of bacteria, fungi, and nematodes across different agricultural practices in coffee agroecosystems in Costa Rica.

Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes

Background Endohyphal microbial communities, composed of bacteria and viruses residing within fungal hyphae, play important roles in shaping fungal phenotypes, host interactions, and ecological functions. While endohyphal bacteria have been shown to influence fungal pathogenicity, secondary metabolism, and adaptability, much remains unknown about their diversity and host specificity. Even less is known about endohyphal viruses, whose ecological roles and evolutionary dynamics are poorly understood. This study integrates genomic and transcriptomic approaches to (1) characterize the diversity of endohyphal bacterial and viral communities in fungal endophytes isolated from Fagus grandifolia leaves, and (2) assess potential host specialization through phylogenetic signal analyses.

We analyzed 19 fungal isolates spanning eight fungal orders (Amphisphaeriales, Botryosphaeriales, Diaporthales, Glomerellales, Mucorales, Pleosporales, Sordariales, and Xylariales). Bacterial communities were
highly diverse and showed significant phylogenetic signal, with core taxa—such as Bacillales, Burkholderiales, Enterobacterales, Hyphomicrobiales, and Pseudomonadales—shared across hosts. Several bacterial groups were associated with specific fungal orders, suggesting host specialization: Moraxellales, Sphingomonadales, and Streptosporangiaceae in Amphisphaeriales; Enterobacterales, Hyphomicrobiales, and Micrococcales in Glomerellales; and Cytophagales in Diaporthales. In contrast, viral communities were less diverse and dominated by double-stranded DNA viruses, primarily Bamfordvirae and Heunggongvirae. No core viral taxa were detected in metatranscriptomic data, and only a few reads of double-stranded RNA viruses were found.

Overall, our results indicate potential host specialization in bacterial endophytes and limited viral diversity in fungal hosts, with dsDNA viruses dominating the endohyphal virome. These findings provide new insights into the ecological and evolutionary dynamics of fungal-associated microbiota. Future work expanding taxonomic reference databases and exploring the functional roles of these microbial symbionts will be essential to understanding their contributions to fungal biology, host interactions, and broader ecosystem processes.

Elevational and seasonal patterns of plant pollinator networks in two highland tropical ecosystems in Costa Rica

Many plant species in high montane ecosystems rely on animal pollination for sexual repro- duction, however, our understanding of plant-pollinator interactions in tropical montane hab- itats is still limited. We compared species diversity and composition of blooming plants and floral visitors, and the structure of plant-floral visitor networks between the Montane Forest and Paramo ecosystems in Costa Rica. We also studied the influence of seasonality on spe- cies composition and interaction structure. Given the severe climatic conditions experienced by organisms in habitats above treeline, we expected lower plant and insect richness, as well as less specialized and smaller pollination networks in the Paramo than in Montane For- est where climatic conditions are milder and understory plants are better protected. Accord- ingly, we found that blooming plants and floral visitor species richness was higher in the Montane Forest than in the Paramo, and in both ecosystems species richness of blooming plants and floral visitors was higher in the rainy season than in the dry season. Interaction networks in the Paramo were smaller and more nested, with lower levels of specialization and modularity than those in the Montane Forest, but there were no seasonal differences within either ecosystem. Beta diversity analyses indicate that differences between ecosys- tems are likely explained by species turnover, whereas within the Montane Forest differ- ences between seasons are more likely explained by the rewiring of interactions. Results indicate that the decrease in species diversity with elevation affects network structure, increasing nestedness and reducing specialization and modularity.

ohun: An R package for diagnosing and optimizing automatic sound event detection

Flexible use of visual and acoustic cues during roost finding in Spix’s disc-winged bat (Thyroptera tricolor)

The ability of an animal to detect environmental cues is crucial for its survival and fitness. In bats, sound certainly plays a signifi- cant role in the search for food, spatial navigation, and social communication. Yet, the efficiency of bat’s echolocation could be lim- ited by atmospheric attenuation and background clutter. In this context, sound can be complemented by other sensory modalities, like smell or vision. Spix’s disc-winged bat (Thyroptera tricolor) uses acoustic cues from other group members to locate the roost (tubular unfurled leaves of plants in the order Zingiberales). Our research focused on how individuals find a roost that has not been yet occupied, considering the urge to find a suitable leaf approximately every day, during nighttime or in daylight. We observed the process of roost finding in T. tricolor in a flight cage, manipulating the audio/visual sensory input available for each trial. A broad- band noise was broadcast in order to mask echolocation, while experiments conducted at night reduced significantly the amount of light. We measured the time needed to locate the roost under these different conditions. Results show that with limited visual and acoustic cues, search time increases significantly. In contrast bats seemed capable of using acoustic and visual cues in a similarly efficient manner, since roost search showed no strong differences in duration when bats could use only sound, only vision, or both senses at the same time. Our results show that non-acoustic inputs can still be an important source of information for finding crit- ical resources in bats.

Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems

The Costa Rican Paramo is a unique ecosystem with high levels of endemism that is geographically isolated from the Andean Paramos. Paramo ecosystems occur above Montane Forests, below the permanent snow level, and their vegetation differs notably from that of adjacent Montane Forests. We compared the composition and beta diversity of blooming plant species using phenological data from functional plant groups (i.e., insect-visited, bird-visited and insect + bird-visited plants) between a Paramo and a Montane Forest site in Costa Rica and analyzed seasonal changes in blooming plant diversity between the rainy and dry seasons. Species richness was higher in the Montane Forest for all plant categories, except for insect-visited plants, which was higher in the Paramo. Beta diversity and blooming plant composition differed between both ecosystems and seasons. Differences in species richness and beta diversity between Paramo and the adjacent Montane Forest are likely the result of dispersal events that occurred during the last glacial period and subsequent isolation, as climate turned to tropical conditions after the Pleistocene, and to stressful abiotic conditions in the Paramo ecosystem that limit species establishment. Differences in blooming plant composition between both ecosystems and seasons are likely attributed to differential effects of climatic cues triggering the flowering events in each ecosystem, but phylogenetic conservatism cannot be discarded. Analyses of species composition and richness based on flowering phenology data are useful to evaluate potential floral resources for floral visitors (insects and birds) and how these resources change spatially and temporarily in endangered ecosystems such as the Paramo.

Landing manoeuvres predict roost-site preferences in bats

Journal of Experimental Biology (2022) 225, jeb244267. doi:10.1242/jeb.244267

Roosts are vital for the survival of many species, and how individuals
choose one site over another is affected by various factors. In bats,
for example, species may use stiff roosts such as caves or compliant
ones such as leaves; each type requires not only specific
morphological adaptations but also different landing manoeuvres.
Selecting a suitable roost within those broad categories may increase
landing performance, reducing accidents and decreasing exposure
time to predators. We addressed whether bats select specific roost
sites based on the availability of a suitable landing surface, which
could increase landing performance. Our study focused on Spix’s
disc-winged bats (Thyroptera tricolor), a species known to roost within
developing tubular leaves. As previous studies show that this species
relies on the leaves’ apex for safe landing and rapid post-landing
settlement, we predicted that bats would prefer to roost in tubular
structures with a longer apex and that landing would be consistently
more effective on those leaves. Field observations showed that
T. tricolor predominantly used two species for roosting, Heliconia
imbricata and Calathea lutea, but they preferred roosting in the
former. The main difference between these two plant species was the
length of the leaf’s apex (longer in H. imbricata). Experiments in a
flight cage also showed that bats used more consistent approach and
landing tactics when accessing leaves with a longer apex. Our results
suggest that landing mechanics may strongly influence resource
selection, especially when complex manoeuvres are needed to
acquire those resources.

End member and Bayesian mixing models consistently indicate near-surface flowpath dominance in a pristine humid tropical rainforest

Hydrological Processes. 2021;35:e14153.

The impacts of forest conversion on runoff generation in the tropics have received much interest, but scientific progress is still hampered by challenging fieldwork conditions and limited knowledge about runoff mechanisms. Here, we assessed the runoff generation, flow paths and water source dynamics of a pristine rainforest catchment in Costa Rica using end-member mixing analysis (EMMA) and a Bayesian mixing model (MixSIAR). Geochemical tracer data collected over a 4-week field campaign were combined with tritium data used to assess potential deeper groundwater flow pathways to the perennial stream. The streamflow composition was best captured using three end-members, namely throughfall, shallow (5–15 cm) and deeper (15–50 cm) soil water. We estimated the end-member contributions to the main stream and two tributaries using the two mixing approaches and found good agreement between results obtained from EMMA and MixSIAR. The system was overwhelmingly dominated by near-surface sources, with little evidence for deeper and older groundwater as tritium-derived baseflow mean transit time was between 2.0 and 4.4 years. The shallow soil flow pathway dominated streamflow contributions in the main stream (median 39% and 49% based on EMMA and MixSIAR, respectively), followed by the deeper soil (32% and 31%) and throughfall (25%and 19%). The two tributaries had even greater shallowsoil water contributions relative to the main stream(83% and 74% for tributary A and 42% and 63% for tributary B). Tributary B had no detectable deep soil water contribution, reflecting the morphology of the hillslope (steeper slopes, shallower soils and lower vegetation density compared to hillslope A). Despite the short sampling campaign and associated uncertainties, this study allowed to thoroughly assess runoff generation mechanisms in a humid tropical catchment. Our results also provide a first comparison of two increasingly used mixing models and suggest that EMMA and MixSIAR yield comparable estimates of water source partitioning in this tropical, volcanic rainforest environment.

Can hydrological drought be efficiently predicted by conceptual rainfall-runoff models with global data products?

Journal of Natural Resources and Development 2021; 02: 01 - 18

The seasonally-dry tropics of northern Costa Rica are characterized by recurrent drought events with negative socio-economic impacts on a vulnerable population. Scarce hydroclimatic observational data constraints reasonable water management and often results in water scarcity issues. 

This study analyses hydrological drought situations using freely available Global Precipitation Products (GPP) and a Regional Climate Model (RCM) that drive a relatively simple, semi-distributed rainfall-runoff model (HBV-Light). Firstly, the GPP and observed rainfall were used to calibrate the model simulating streamflow dynamics. Secondly, drought detection and estimates of drought duration, intensity and severity were determined with a daily variable threshold approach. Thirdly, we developed future hydrological drought scenarios based on a RCM. Generally, the GPP CHIRPS (Climate Hazards Group InfraRed Precipitation with Station Data) resulted in the best streamflow simulations (KGE > 0.6) compared with the model driven by observed rainfall (KGE > 0.7). CHIRPS also correctly identified the observed streamflow drought periods of 1994, 1997-1998 and 2001-2002. Average observed streamflow drought severity was 27.9 mm compared to the CHIRPS-derived severity of 20.6 mm (error estimate of Å}7.3 mm). The model in combination with global data can be successfully used to identify drought periods and their duration, but model uncertainty currently prevents from forecasting streamflow deficit with volume errors below 50%.

The future hydrological drought scenario showed more severe drought periods between 2039-2041 and 2042-2043. This study responds to the need for drought assessments in the seasonally-dry tropics with scarce observations as a tool for adaptation to climate change and water resource management.

Informe de resultados del Estudio de Opinión Sociopolítica