Functional Redundancy Research Articles

Abstract Tidal freshwater wetlands are critical for removing or sequestering watershed‐derived nitrogen loads before they reach the coast, where they can lead to eutrophication. However, rising seas and increasing climate variability will alter important physicochemical parameters that control nitrogen generation (e.g., nitrogen fixation) and removal processes (e.g., denitrification) in these habitats. Furthermore, the frequency and timing of these changes could vary from short, finite pulses during a storm or drought to long‐term presses from sea level rise, which may differentially affect biogeochemical cycling. We used intact core mesocosms to examine how microbial community structure and nitrogen cycling changed in response to increased temperature and salinity under pulse and press disturbances. We found that net N 2 flux rates, defined as the balance between nitrogen fixation, which adds nitrogen, and denitrification, which removes it, did not directionally change in response to stressor pulse or press. Instead, it became more variable under both disturbance regimes, underscoring the importance of both denitrification and nitrogen fixation in these systems. Nitrous oxide production rates, however, decreased and became more stable over time in the press scenario but remained highly variable in the pulse scenario. Under both pulse and press disturbance, both the overall and the active component of the microbial community changed, particularly in response to the salinity treatment. Although there was an overall community shift, core members of the microbiome capable of denitrification and nitrogen fixation persisted. Both pulses and presses of temperature and salinity changed the microbial communities of tidal freshwater wetlands, but a combination of microbial resistance and functional redundancy appears to allow important N cycling processes to persist. These findings provide valuable knowledge on the functional and structural potential of the nitrogen cycling microbial communities in tidal freshwater wetlands when facing future climate variability.

Insects depend on sophisticated olfaction for survival. The diamondback moth (Plutella xylostella), a devastating pest with rapid reproduction and insecticide resistance, requires novel control strategies. However, its odor recognition mechanisms, particularly for host-emitted α-Humulene, remain unclear. We investigated two odorant receptor genes, PxOR28 and PxOR31, which are highly expressed in female antennae. Cloning, qPCR, and CRISPR/Cas9 knockout demonstrated their essential role in mediating behavioral attraction to α-Humulene for oviposition. While α-Humulene activated wild-type antennae and attracted moths, mutants lacking both receptors exhibited no response, indicating functional redundancy. These findings elucidate P. xylostella's perception of α-Humulene and highlight chemosensory receptors or key odorants as targets for sustainable pest control.

Abstract Background and Aims Long-lasting changes in soil biodiversity and chemistry reflecting past land use are commonly found during the conversion between natural and agricultural systems . However, no clear pattern can be seen when rotating crops are established. Most studies focus on arable systems and over short-term rotations, neglecting longer-term tree-crop successions. We hypothesised that converting one long-term tree crop to another would retain a stronger relationship between soil chemistry, biodiversity, and agricultural history. Methods We selected a unique agricultural field enclosed in less than one hectare and characterised by three similar neighbouring sites where viticulture was replaced by apple cultivation in 1922, 1970 and 2016. This specific agronomic context allowed us to investigate the possible long-term effect of tree-crop succession on soil chemistry and soil biodiversity (Bacteria, Fungi, Animalia, and Protozoa), avoiding biases due to pedo-climatic variability. Results Our results indicate the soils are physicochemically and biologically distinguishable based on tree-crop conversion. Mainly, we identified a decrease in clay and silt from 1922 to 2016, alongside a decline in keystone species, while microbial and animal communities grouped in three clear different clusters. Nevertheless, no significant changes were observed in soil functionality, likely due to the high functional redundancy within microbial communities. Conclusion Our findings highlight the lasting impact of tree-crop conversion, underscoring the importance of considering long-term agricultural history when assessing soil agricultural management.

Chronic and neuropathic pain remain significant clinical challenges owing to limited efficacy and safety concerns associated with conventional analgesics, including opioids and NSAIDs. Voltage-gated sodium channels, particularly Nav1.7 and Nav1.8, have emerged as promising non-opioid targets for pain modulation, given their selective expression in peripheral nociceptors and critical roles in pain signal transmission. Recent advances in structural biology and pharmacology have enabled the development of highly selective inhibitors targeting these channels. This review explores sodium channel inhibitors currently in clinical development, with a focus on suzetrigine (VX-548), the first US Food and Drug Administration (FDA)-approved Nav1.8 inhibitor for acute pain, as well as other investigational agents such as ralfinamide, OLP-1002, LTGO-33 and HBW-004285. Despite setbacks in early candidates owing to selectivity and tolerability issues, ongoing trials demonstrate renewed optimism for a new class of analgesics that may overcome the limitations of traditional pain therapies. We discuss key pharmacological challenges observed in earlier trials including functional redundancy, species differences, and on-target side effects, and outline how emerging strategies, such as structural biology-guided design, combination therapies, and precision medicine, are paving the way for safer, more effective, nonaddictive pain treatments.

The extracellular matrix (ECM) provides structural support and dynamic signaling cues, governing cellular behavior and tissue integrity. ECM remodeling, critically regulated by irreversible proteolysis, profoundly impacts development, homeostasis, and disease. This review examines the major families of ECM-degrading proteases-matrix metalloproteinases (MMPs), serine proteases, a disintegrin and metalloproteinases (ADAMs), metalloproteinase with thrombospondin motifs (ADAMTSs), and cysteine proteases-emphasizing their shared regulatory mechanisms and proteolytic activity in reshaping the tissue microenvironment. These proteases exhibit functional redundancy, particularly in the generation of matrikines, growth factors, and cytokines from common ECM substrates, all contributing to ECM softening. These overlaps in substrates and the resulting bioactive molecules amplify proteolysis within the tissue. The generated matrikines, growth factors, and cytokines further drive ECM remodeling through feedback loops, influencing the expression and activation of proteolytic enzymes. Despite these shared mechanisms, protease families demonstrate cell-specific functional specialization shaped by transcriptional programs, microenvironmental signals, and subcellular targeting, ensuring precise spatiotemporal proteolysis during processes such as development, wound healing, and immune responses. Dysregulation of this intricate proteolytic network contributes to chronic pathologies and cancer. Thus, understanding and targeting these processes is crucial for therapeutic intervention and the improved regulation of biological functions. Collectively, these insights reveal how irreversible ECM proteolysis orchestrates complex, context-dependent biological responses in both health and disease.

Pan-genome analysis of the LATERAL ORGAN BOUNDARIES domain family in camelina and function investigation of LATERAL ORGAN BOUNDARIES domain 40 in fatty acid synthesis.

The role of signaling lymphocytic activation molecule (SLAM) family receptors in health and disease progression: Focusing on cancer and therapy.

Trawling the archives: Long-term trends in fish taxonomic and functional diversity in UK coastal community.

Close interactions between prokaryotes and plasmids or viruses highlight a pivotal role of horizontal gene transfer in shaping antibiotic/metal(loid) resistome and their prokaryotic supercarriers in untreated hospital sewage.

Modified biochar mitigates nitrogen loss in distilled grain waste composting by modulating microbial community assembly and function.

Distinct adaptation strategies and functional potentials of abundant and rare prokaryotes across seasonal dynamics and long-term eutrophication in Xiangshan Bay.

Insect establishment and dispersal are often influenced by temperature, with gut microbiota playing a critical role in host adaptation to environmental stress. This study investigated how gut bacterial structure and function in the invasive red-haired bark beetle (RHB), Hylurgus ligniperda (Fabricius) respond to temperature fluctuations, focusing on three core culturable bacteria: Rahnella perminowiae, Serratia marcescens, and Hafnia psychrotolerans. We found that temperature variations induced specific structural changes in the gut bacterial community, which in turn affected key functional processes such as carbohydrate metabolism. Notably, the relative abundance of Rahnella increased by more than 10% during the cold period (CP), and it maintained stable production of proteases and lipases under low temperatures—a trait that may be crucial for supporting host development in cold environments. Feeding on the diet converted by R. perminowiae at 5 °C resulted in a 20.9-day reduction in pupation time and a 1.8-fold increase in adult body mass compared to the blank control group, respectively. We propose that temperature remodels the gut microbiota by modulating competitive relationships among functional bacteria. This regulatory mechanism, based on functional redundancy and dynamic balance, serves as a buffer strategy that aids insect adaptation to temperature changes. Our findings provide new insights and a theoretical foundation for understanding pest outbreak patterns under climate warming and developing microbe-targeted control strategies.

Bacillus subtilis is able to catabolize fructosamines, also known as Amadori rearrangement products. The frlBONMD-frlP operon mediates this process and is subjected to specific and global regulation. Although the degradation pathway favoring α-glycated amino acids is known, the mechanisms of substrate uptake have remained unclear. In this study, mutagenic and functional analyses revealed that FrlONM, a type I ABC importer, along with the nucleotide-binding domain (NBD) FrlP, is required for the uptake of fructosevaline. Transcriptional and translation frlP-lacZ fusions indicated that frlP is induced by fructosevaline and negatively regulated by the FrlR repressor. In addition, we show that MsmX, a multitask NBD of B. subtilis, is also able to serve as an energy motor of this type I ABC importer and that its presence alongside FrlP is vital for optimal growth on fructosevaline. To address the physiological significance of this functional redundancy, we assessed the distribution of ABC type I NBDs FrlP and MsmX across the Bacillaceae family. MsmX is homogeneously distributed in the Bacillaceae family tree, while FrlP is restricted to the Bacillus subtilis group, suggesting that the presence of FrlP together with other components of the fructosamines operon is important for bacterial fitness in plant-associated ecological niches.IMPORTANCEBacillus subtilis is widely applied in the industry as a microbial cell factory, as a biofertilizer for sustainable agriculture, in the animal feed industry and as human probiotic. In its natural environment, B. subtilis helps to shape the gut microbiome and the phytomicrobiome. Fructosamines, or Amadori rearrangement products, are ubiquitously found in nature and serve as precursors of toxic cell end-products implicated in the pathology of human diseases. This study provides a solid contribution to a deep knowledge of transport mechanisms, genetic regulation, and physiological relevance of fructosamines utilization in B. subtilis. Moreover, it highlights an unusual strategy to adapt to alterations in nutrient availability by swapping the energy providing domain of ABC transporters.

High-turbidity rivers, exemplified by the Yellow River, face significant ecological risks due to anthropogenic water-sediment regulation (WSR), which disrupts sedimentary habitats and biogeochemical cycles. However, the stage-specific impacts of WSR on microbial community structure, network complexity, and biogeochemical functions in reservoir-river continua remain poorly understood. In this study, we investigated microbial responses across different WSR stages in the Xiaolangdi Dam reservoir-river continuum using an integrated approach, including 16S rRNA gene sequencing, molecular ecological network analysis (MENs), and hierarchical partitioning. The results showed that WSR induced transient but profound shifts in microbial communities. The sediment-regulation stage (Inter_WSR3) exerted the strongest disturbance, characterized by peak turbidity (77.80 NTU), nutrient fluxes (NO 3 − = 3.10 mg/L), and sediment resuspension, which restructured surface sediment (SS) communities dominated by copiotrophic Gammaproteobacteria (35.69%) and Bacteroidia (14.82%). Microbial α-diversity transiently increased during WSR but recovered to baseline levels post-disturbance, masking β-diversity divergence driven by niche differentiation. Molecular ecological networks exhibited peak complexity (nodes = 1,318; modularity = 0.73) during Inter_WSR3 but failed to recover Post_WSR, reflecting weakened functional redundancy and ecosystem resilience. Hierarchical partitioning identified stage-specific drivers: chlorophyll a (Chla) dominated SS assembly during Inter_WSR3, while nitrate (NO₃ − ) and turbidity governed particle-attached (PA) and free-living (FL) communities. Light limitation and sediment-water interactions overrode dissolved oxygen and temperature as primary drivers in the Yellow River. These findings reveal that WSR disrupts microbial co-occurrence patterns and functional redundancy, with lasting consequences for ecosystem services. To reconcile sediment management with ecological sustainability, we advocate phased WSR implementation, targeted monitoring of FL/PA communities, and habitat restoration to enhance connectivity. This study advances the mechanistic understanding of high-turbidity river ecology and provides actionable insights for global river management.

Cities operate as complex socio-spatial systems, composed of interconnected networks formed by diverse physical and social components. Dynamic interactions among these components sustain the city’s functionality, support the fulfilment of fundamental human needs, and ultimately determine the quality of life for urban residents. Urban resilience to earthquakes is traditionally assessed through physical damage analyses, yet such evaluations often overlook human-centred impacts on the quality of life. This study introduces a novel framework for evaluating the accessibility of citizens to essential urban functions post-earthquake, with these functions assessed through access to the corresponding facilities, and emphasising human needs rather than mere structural vulnerability. The proposed approach integrates seismic fragility assessments with graph theory-based accessibility metrics, capturing how damage to buildings and road blockages caused by earthquake-induced building debris affect the ability of residents to access vital urban functions. By integrating a panel of experts, the research examines the shifts in the hierarchy of human needs following seismic events. The proposed model is tested on a case study of a small Mid-European town under different seismic scenarios and evaluation approaches. The analysis shows that strong earthquakes can result in severe fragmentation of the urban network, with up to one-third of the population losing access to essential services. Educational and work-related functions emerge as particularly vulnerable, while healthcare accessibility proves more stable due to spatial distribution and facility robustness. Findings reveal a critical distinction between structural and functional vulnerability. A city may preserve most of its physical structures but still suffer major functional collapse if key services become inaccessible. This distinction underscores the need for spatial strategies that ensure the redundancy and dispersion of critical urban functions, particularly in historically dense or infrastructure-dependent areas. Building upon these findings, this study offers a methodology for assessing urban resilience by prioritising accessibility and human needs, aiding planners in improving emergency preparedness and long-term recovery.

The progressive shift in anaerobic digestion communities under extreme propionate levels led to a redundant microbiome capable of producing methane.

Therapeutic compounds exert impacts on gut microbiota; however, how they affect the community functional ecology, especially as reflected at the protein level, remains largely unexplored. In this study, we systematically map metaproteomic responses of ex vivo human gut microbiota to 312 compounds, generating 4.6 million microbial protein responses, available as an interactive resource (https://shiny.imetalab.ca/MPR_Viz/). Protein-level analyses identify significant metaproteomic shifts induced by 47 compounds, with neuropharmaceuticals as the sole drug class significantly enriched among these hits. Further analyses on the community level reveal a tri-stability pattern in microbial composition and the emergence of three distinct functional states, based on a functional beta-diversity metric. Notably, neuropharmaceuticals cause particularly strong effects on the microbiomes, lowering the proteome-level functional redundancy and raising the level of antimicrobial resistance proteins, ultimately pushing the microbiome into an alternative functional state. Preliminary validation suggests that enhancing functional redundancy may contribute to maintaining microbiota resilience against neuropharmaceutical-induced antimicrobial resistance. Overall, this work establishes a comprehensive view of how drugs influence gut microbiome function and ecology at the protein level, proposes a landscape-based framework for interpreting community resilience, and highlights the need to consider protein-level and ecological responses in the evaluation of therapeutic interventions.

Tudor domain-containing proteins (TDRDs) constitute an evolutionarily conserved protein family and are critical for germline development and piRNA pathway regulation, with established roles in male fertility. While multiple TDRD family members have been functionally linked to spermatogenic impairment, the precise biological role of TDRD15 remains to be elucidated. We used CRISPR/Cas9-mediated gene editing to generate Tdrd15 knockout (KO) golden hamsters (Mesocricetus auratus), a model necessitated by the absence of a functional Tdrd15 ortholog in the mouse genome, to investigate its function in male reproduction. Phylogenetic analysis demonstrated that TDRD15 is strongly conserved among eutherian mammals, with testis-restricted expression patterns in hamsters. Despite the successful induction of frameshift mutations and significant transcriptional knockdown, Tdrd15 KO males maintained normal fertility parameters, including unaltered testicular architecture, spermatogenic progression (confirmed by periodic acidic-Schiff (PAS) staining and immunohistochemistry), and sperm quality metrics determined using a computer-assisted analysis. Quantitative polymerase chain reaction (qPCR) revealed compensatory overexpression of paralogous Tdrd genes in KO testes, implying functional redundancy within this protein family. This study provides the first experimental evidence that TDRD15 is dispensable for male fertility in golden hamsters under physiological conditions, thereby challenging the prevailing assumptions of its obligatory function in spermiogenesis. Altogether, these findings support a more targeted allocation of research efforts within the field of male reproductive biology.

Moso bamboo (Phyllostachys heterocyclas) has rapidly expanded in subtropical broadleaf forests of eastern China, raising concerns about biodiversity loss and community restructuring. We investigated how the expansion of this native bamboo influences species diversity and phylogenetic diversity across forest strata (trees, shrubs, herbs) by surveying 16 plots along a gradient from bamboo-free to bamboo-dominated stands. We measured soil properties, calculated multiple α-diversity indices, and constructed a community phylogeny to assess phylogenetic metrics. We also constructed a phylogenetically informed Resistance Index (RI) to evaluate species-specific responses to bamboo expansion. The results showed that overstory tree species richness and Faith’s phylogenetic diversity declined sharply with increasing bamboo cover, accompanied by significant losses of evolutionary lineages. In contrast, understory shrub and herb layers exhibited stable or higher species richness under bamboo expansion, although functional redundancy among new colonists suggests limited gains in ecosystem function. Soil conditions shifted substantially along the expansion gradient: pH increased by approximately 0.5 units, while total organic carbon and total nitrogen each decreased by about 30% (p < 0.01). Redundancy analysis and variance partitioning indicated that bamboo’s impacts on community diversity are mediated primarily through these soil changes. Species-level trends revealed that formerly dominant canopy trees (e.g., Schima superba, Pinus massoniana) were highly susceptible to bamboo, whereas certain shade-tolerant taxa (e.g., Cyclobalanopsis glauca, Rubus buergeri) showed resilience. In conclusion, the aggressive expansion of Moso bamboo drastically alters multi-layer forest diversity and community assembly processes. Our findings point to a need for targeted management (e.g., reducing bamboo density, soil restoration, and enrichment planting of native species) to mitigate biodiversity loss, underscoring the importance of considering phylogenetic diversity in expansion ecology and forest conservation.

Wastewater treatment plants (WWTP) are a crucial part of modern day infrastructure, cleaning about half of our global wastewater. However, the emergence of micropollutants and higher frequencies of extreme weather events pose unprecedented challenges for society and biodiversity. Conventionally treated wastewater and altered flow regimes create environmental boundaries in rivers, impacting aquatic communities. Previous studies revealed pronounced taxonomic changes in freshwater invertebrate communities in response to WWTP effluents. To explore whether these shifts extend to functional diversity, we studied 338 communities upstream and downstream of 169 WWTPs using commonly applied functional diversity metrics. Surprisingly, we found no clear changes in functional alpha and beta diversity metrics, or community weighted means (CWM), suggesting that trait redundancy offsets the functional impact of the previously observed species turnover. However, in streams dominated by Ephemeroptera, Plecoptera and Trichoptera (EPT), we found more pronounced shifts in CWMs, indicating that the extent of functional changes depends on the baseline condition of the streams. EPT-dominated site-pairs showed significant shifts in traits related to reproduction, dispersal, and feeding, including increased occurrences of ovoviviparity and interstitial locomotion potentially as an avoidance mechanism of high flow and low oxygen saturation. Further, shifts in shredding and absorbing feeding types, aquatic passive dispersal, and hololimnic life cycles might be forms of adaptation to increased nutrient concentrations and reduced intermittency induced by WWTPs. These findings demonstrate that functional responses to wastewater inputs can remain undetected due to the noise inherent in large datasets and are often absent as a result of functional redundancy. In contrast, significant changes emerge in communities dominated by sensitive species, underscoring the value of trait-based approaches for detecting context-dependent ecological impacts.