Microbial Diversity as the Next Frontier of Payments for Ecosystem Services in Nature-Positive Finance

Microbial Diversity as the Next Frontier of Payments for Ecosystem Services in Nature-Positive Finance | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 21 January 2026 V1 Latest version Share on Microbial Diversity as the Next Frontier of Payments for Ecosystem Services in Nature-Positive Finance Authors : Kohei Ito 0000-0001-8267-4495 [email protected] , Honami Ando 0009-0008-1757-6117 , and Hiroshi Honda 0000-0002-2936-2617 [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.176901865.58628984/v1 Published npj Biodiversity Version of record Peer review timeline 296 views 104 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Payments for Ecosystem Services (PES) have matured across forests (carbon), watersheds (water quality and quantity), agricultural landscapes (biodiversity), and urban stormwater management. Most biodiversity assessments emphasize insects, fish, and birds. By contrast, schemes that directly measure and reward the diversity of microbial communities-the foundations of ecosystem services in soils, aquatic systems, and urban green spaces-remain scarce. Meanwhile, the Kunming-Montreal Global Biodiversity Framework calls for mobilizing at least USD 200 billion per year by 2030, and the Global Biodiversity Framework Fund has launched; but current flows into PES are limited, and PES explicitly targeting microbes is largely uncharted. This Perspective argues that microbially focused PES is rare and, even when they exist, they tend to be biased toward specific pathogens or pollution indicators. However, measurement, reporting, and verification of various microorganisms are operationally feasible and methods to strengthen source attribution and contribution estimation are now mature; and that channeling a share of Nature-Positive finance to microbial ecosystem assessments could jointly advance drinking-water safety, soil health, agricultural resilience, and urban public health. We discuss the importance of microbial-PES in conserving and enhancing ecosystem services. MAIN TEXT INTRODUCTION Driven by the global push toward “Nature Positive,” the importance of biodiversity assessment is rising. The GBF asks Parties to mobilize at least USD 200 billion per year from all sources by 2030, including USD 30 billion per year in international finance [1], and the Global Biodiversity Framework Fund (GBFF) has been launched, reaching pledges of roughly USD 386 million by mid-2025 [2]. In parallel, corporates are beginning to disclose nature-related interfaces and risks through frameworks such as the TNFD [3]. PES is an outcome-oriented mechanism in which beneficiaries (e.g., utilities, municipalities, developers, consumers) make conditional payments to ecosystem-service providers (e.g., landowners, communities, protected-area managers) [4]. Typical examples include water tariffs financing upstream forest conservation [5], premium pricing for biodiversity-friendly agriculture [6], and carbon finance funding mangrove protection [7]. These well-known PES cases demonstrate effectiveness, and integrating PES with Nature-Positive capital could further stabilize service provision. However, relying solely on visible taxa and habitats—forests, wetlands, birds, fish—fails to capture the foundational mechanisms linking biodiversity, ecosystem services, and human health. This macro-centric view overlooks the “invisible biota” that underpin virtually all life-support systems: microbial diversity. Microbes inhabit every environment on Earth, from natural ecosystems to urban settings, and would drive carbon and nitrogen cycling, water purification, soil fertility, agricultural resilience, human health regulation, and even verification of food characteristics, safety, and quality (Figure 1). Elevating microbial communities to outcomes within PES would value foundational functions long overlooked and enable durable finance for natural capital. This Perspective reviews current PES targets, examines the opportunity to center microbes, and sketches institutional designs that braid Nature-Positive finance with microbial-PES. What Does PES Currently Pay For? PES schemes worldwide have largely targeted biota and services that are visible and socially legible (Table 1). In forests, carbon sequestration by tree communities and emblematic biodiversity (forest birds, large mammals) take center stage, as in Costa Rica’s national PES (financed by a fuel tax since 1997) and Mexico’s PSAH (Programa de Servicios Ambientales Hidrológicos) for hydrological services [8,9]. In watersheds, outcomes include turbidity, nutrients, and drinking-water safety. The New York City Catskills program is emblematic: rather than build a costly filtration plant, NYC pays for upstream land-management improvements under the Filtration Avoidance Determination (FAD) [5]. Water funds such as Quito’s FONAG and Vittel’s source-water protection are likewise canonical [10]. In agricultural landscapes, iconic rice-paddy fauna (dragonflies, frogs) and farmland birds feature prominently; Japan’s Toki- and Stork-friendly farming are well known [11], and EU agri-environment schemes (AES) support biodiversity via direct payments [12]. In wetlands and mangroves, attention centers on mangrove forests, benthic fauna, and migratory birds; Kenya’s Mikoko Pamoja—the first community-led blue-carbon credit project—has become internationally influential [13]. Urban programs link trees, rain gardens, and green roofs to stormwater retention and heat-island mitigation; Washington, DC’s Stormwater Retention Credit market [14] and Philadelphia’s crediting scheme monetize retention performance [15]. Marine PES analogs focus on coral reefs, seagrass, turtles, and herbivorous fish, with user-fee models in Bonaire [16]. Across these cases, target biota cluster around trees, farmland flagship species, riverine and wetland fish and waterbirds, coastal corals and seagrasses, and urban birds and insects—i.e., high-visibility assemblages. Indicator sets likewise emphasize simplified metrics: tons of carbon, forest cover, turbidity, nutrients, runoff volume, and amenity value. By contrast, linking microbial diversity and function in soils and waters directly to payments remains rare. Consequently, current frameworks tend to address microbes solely as risks to be managed (e.g., pathogens), overlooking the opportunity to leverage diverse microbiomes for proactive health promotion. If scientifically grounded indicator species including those from microbial communities can be identified, monitored, and translated into measurable metrics, PES schemes have the potential to evolve from reactive risk management to instruments that actively advance both ecosystem integrity and human health. The Current State of “Microbial PES” Where PES (or cognate schemes) engage microbes, evaluation axes overwhelmingly prioritize drinking-water safety and sanitary risk via pathogens and fecal indicator bacteria (FIB), with few cases that explicitly include community-level diversity or functional metrics (Table 2). Even in flagship programs like NYC’s [5], performance metrics are strictly limited to specific pathogens and FIB, excluding community-level diversity or functions. In Bolivia’s Watershared, a randomized controlled trial was used to evaluate whether incentives for land-use improvements could increase microbial water quality; however, evaluation still centers on a single FIB (E. coli) [17]. Latin American Water Funds (e.g., FONAG; FORAGUA) route city and corporate finance to upstream conservation with outcomes in flow and water quality, but microbial diversity and functions remain outside contractual metrics [10,18]. In cities, green stormwater infrastructure (GSI) (rain gardens and constructed wetlands) often tracks log reductions in FIB at outfalls, with performance varying by site and design; microbial diversity/function is monitored, if at all, as a supplementary indicator rather than an outcome [19,20]. Overall, current “microbe × PES” framework functions solely from the perspective of mitigating the negative impacts of specific microbes. Microbial community diversity and functional diversity, however, have been associated with health-relevant outcomes [21,22]. Contact with natural environments alters the human microbiome, supports immune development, and is thought to reduce the risk of immune-related diseases [23]. Thus, in urban development, attention should not be limited to visible biological communities; maintaining and conserving native microbial assemblages is considered important for human health care. This aligns with the “biodiversity hypothesis,” which suggests that contact with diverse environmental microbiota regulates immune function and reduces the risk of non-communicable diseases. However, current PES frameworks remain reactive, focusing almost exclusively on “defense” (mitigating pathogen risks) while ignoring the potential for “offense” (actively promoting immune resilience through exposure to microbial diversity). Consequently, frameworks that explicitly value and pay for these health-promoting microbial functions are virtually nonexistent. Why Extend PES to Microbes? Current PES targets visible ecosystems and macro-biota, and relies on carbon, hydrologic metrics, or minimal sanitary indicators (e.g. FIB). As the ubiquitous engines of biogeochemical cycles, microbial communities in soils and waters drive the regulation, provisioning, and supporting services that sustain human well-being. Therefore, extending PES to these “invisible engines” is a necessary step toward capturing function and resilience more directly. First, microbial diversity underpins ecosystem stability. Diverse soil communities conduct decomposition and nitrogen cycling; higher diversity buffers function under stressors such as drought and temperature variability [24]. This stability will elevate agricultural productivity and watershed retention while reducing erosion and sustaining long-term carbon storage, bringing the “invisible foundation” of soils into scope for PES. Second, adding microbial community metrics to source-water and distribution systems can refine drinking-water safety assessment. While a single FIB monitoring provides minimum safeguards but remains insufficient for water safety [25], microbial community–based monitoring would be a promising viewpoint for health and early anomalies [26], moving payments beyond “compliance” to durable guarantees of water quality. Third, soil microbes link directly to carbon sequestration and agricultural resilience. Through stabilization of soil organic carbon and aggregation, microbes would facilitate carbon storage, nutrient provisioning, and disease resistance—jointly benefiting climate mitigation and food security [27]. Fourth, credible measurement, reporting, and verification (MRV) is essential. Technologies like Microbial Source Tracking (MST) [28] and shared Amplicon Sequence Variant (ASV) analysis [29,30] now enable precise causal attribution and the tracking of functional linkages across environments. Integrated with traditional pathogen indicators, these methods allow PES to evidence both risk reduction and functional recovery. However, advancing microbial-PES requires systematic meta-comparison of microbial community structures across ecosystems, together with refined identification of taxa most relevant to water quality and public health. Consolidating this knowledge base is crucial to operationalize microbial indicators as reliable outcome metrics for PES schemes. Finally, extending microbial PES in urban development can couple environmental and public-health goals. Green infrastructure can reduce FIB during storm events [31] while enriching human exposure to diverse environmental microbiota, with potential benefits for allergy and autoimmune risk reduction [23,32]. In recent years, the idea of using “Microbiome rewilding” to address public health issues in cities has been proposed [33]. This concept views green infrastructure as a source of microbes. In this sense, urban PES has the potential to evolve into a mechanism that simultaneously “purchases” both conventional sanitary protection and preventive health promotion. Adopting this perspective would enable investments by municipalities and corporations to simultaneously realize dual benefits in environmental improvement and public health enhancement. To advance this framework, epidemiological investigations are required to clarify how the spatiotemporal distribution of urban microbial communities relates to patterns of human disease incidence, and to define appropriate forms of microbial exposure in terms of both quantity and quality. Nature-Positive Finance: Where Is It Flowing? In recent years, propelled by the “Nature Positive” agenda and GBF targets, private investment in biodiversity and natural capital has surged. UNEP FI reports nature-related finance exceeded USD 100 billion in 2024, growing over 10-fold since 2020 [34]. Nevertheless, achieving the GBF’s 2030 targets will still require additional investment, and a substantial funding gap persists. Within these flows, capital that directly links to PES remains only a small fraction of the total. Syntheses of nature‑based solutions finance suggest that private finance flowing specifically into PES schemes is low single‑digit billions [34–36], i.e. a minor share of total nature‑related flows. Recent PES programs heavily reliant on public and donor funding, underscoring their currently peripheral role within the broader landscape of nature finance [37]. By sector, the largest volumes are directed to forest restoration, coastal and marine conservation, and sustainable agro-forestry projects [38]. These activities align with Nature-Positive objectives, but their performance indicators tend to privilege visible outputs such as hectares planted or expansion of protected areas. By contrast, initiatives that set ecosystem services themselves—for example, water-resources management or improvements to agricultural landscapes—as contracted outcomes remain smaller in scale, and long-term, performance-linked PES designs are still in the minority [39]. As highlighted by the OECD, institutional constraints also inhibit the scaling of PES, as it emphasizes that expanding biodiversity-positive subsidies and PES is essential, emphasizing that standardized and transparent MRV of outcomes is key to mobilizing private capital [36]. In addition, new policy frameworks are emerging—such as the European Union’s consideration of “nature credits” [40]—and these may enable the redirection of nature-related investment into PES structures [41]. The global vision of “Nature Positive,” when it explicitly incorporates microbial community diversity, can function in a more One Health–oriented manner and contribute to the design of ecosystems in which humans, animals, and plants can coexist in a healthy state. Accordingly, we argue that explicit consideration of microbial diversity is essential in the development and implementation of nature credits. Crucially, integrating microbial metrics offers a pathway to unlock private capital. By visualizing hidden risks—such as potential pathogen outbreaks or unseen soil degradation—microbial indicators provide the rigorous data that investors require to manage long-term liabilities. Thus, shifting to a “microbial-inclusive” PES does not merely expand the scope of conservation; it transforms environmental ambiguity into tangible asset performance, serving as a catalyst for robust Nature-Positive investment. Conclusion We reviewed the state of PES, highlighting the paucity of frameworks that target microbial communities. Existing programs focus on visible ecosystems, with indicators centered on carbon and FIB. However, bringing microbial diversity and functions into outcome sets would be essential to assess resilience and public value accurately. In water systems, community metrics can sharpen safety assurance; in soils and agriculture, they can tie payments to carbon sequestration, fertilizer efficiency, and drought tolerance; and in cities, green infrastructure can enrich environmental microbiota alongside sanitary gains (Figure 1). Robust MRV can quantify sources and causal links, making dual benefits (“risk reduction” plus “functional recovery”) visible and auditable. Although Nature-Positive capital is expanding, PES-linked flows are still limited. Embedding microbially grounded outcomes can redirect investment from solely visible assets to the invisible foundations. This shift allows PES to function as a comprehensive health investment instrument, integrating benefits across water safety, agricultural resilience, and human immune health. Author contributions: KI and HH conceived this paper while discussing the significance of monitoring microbial diversity and developing it into an indicator. KI, HA and HH drafted the manuscript, made revisions, and finalized it. Funding: Competing interests: KI and HA belong to a company related to microbial diversity. HH has been participated in developing strategy for this paper as an independent researchers and principal constructor. DATA AVAILABILITY Not applicable. SUPPLEMENTARY MATERIALS There are no supplementary materials. REFERENCES [1] CONVENTION ON BIOLOGICAL DIVERSITY (CBD), DECISION ADOPTED BY THE CONFERENCE OF THE PARTIES TO THE CONVENTION ON BIOLOGICAL DIVERSITY 15/4. Kunming-Montreal Global Biodiversity Framework, 2022. [2] GEF, Global Biodiversity Framework Fund , https://www.thegef.org/what-we-do/topics/global-biodiversity-framework-fund. [3] TNFD, Recommendations of the Taskforce on Nature-related Financial Disclosures, (2023). [4] S. Wunder, Payments for Environmental Services: Some Nuts and Bolts (2005). 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Ranger, Financing Nature-Based Solutions for Adaptation at Scale: Learning from Specialised Investment Managers and Nature Funds, 2023. [36] OECD, Scaling Up Biodiversity-Positive Incentives, Scaling Up Biodiversity-Positive Incent. (2025). [37] T. A. T. Le, K. Vodden, J. Wu, R. Bullock, and G. Sabau, Payments for ecosystem services programs: A global review of contributions towards sustainability, Heliyon 10 , e22361 (2023). [38] C. Van Leenders and D. Heijblom, STRATEGIES TO SCALE-UP PAYMENTS FOR ECOSYSTEM SERVICES, 2024. [39] S. Izquierdo-Tort, S. Jayachandran, and S. Saavedra, Redesigning payments for ecosystem services to increase cost-effectiveness, Nat. Commun. 2024 151 15 , 9252 (2024). [40] European Commission Launches Roadmap towards Nature Credits, Claudia Harper , https://sustainablefutures.linklaters.com/post/102kry8/european-commission-launches-roadmap-towards-nature-credits. [41] EU Looks to “nature Credits” to Fill Green Funding Gap | Reuters , https://www.reuters.com/sustainability/climate-energy/eu-looks-nature-credits-fill-green-funding-gap-2025-07-07/. Figure 1. From Pathogen Control to Health Promotion: Harnessing micro-diversity in PES. Conceptual diagram illustrating how evaluating microbial diversity at the foundation of the ecological pyramid improves outcomes across ecosystem services and human well-being. While traditional frameworks focus on visible biota and mitigating sanitary risks (e.g., pathogens/ fecal indicator bacteria (FIB)), integrating microbial community metrics captures the foundational drivers of ecosystem services. This approach enables a transition from reactive “defensive” risk management to proactive “offensive” health promotion and resilience. This cover has been designed using resources from Flaticon.com. Table 1. Representative PES cases by ecosystem type, focal biota, key services, and examples. FAD: Filtration Avoidance Determination Ecosystem type Focal biota most often targeted Key services / outcome metrics Representative PES cases Forests (temperate/tropical) Tree communities; forest birds; large mammals Carbon sequestration & storage; water regulation; erosion control; biodiversity Costa Rica national PES (FONAFIFO) [8]; Mexico PSAH (hydrological services) [9] Watersheds / drinking water sources (rivers, lakes, aquifers) Riparian vegetation; aquatic insects; freshwater fish; wetland birds Drinking-water quality; baseflow/quantity; sediment control NYC Catskill–Delaware watershed (FAD) ; Quito Water Fund, FONAG; Vittel (France) user-financed PES [5] [10] Agro-ecosystems (paddy landscapes, grasslands) Paddy fauna (dragonflies, frogs); farmland birds; grassland flora Farmland biodiversity; flood mitigation (paddy retention); cultural landscape Sado “Crested Ibis–certified rice” (Japan); Toyooka “Stork-friendly farming” (Japan); EU agri-environmental eco-schemes [11] [12] Wetlands & mangroves (blue carbon) Mangrove forests; benthic invertebrates; shorebirds Blue-carbon storage; coastal protection; water purification; nursery habitat Mikoko Pamoja (Kenya) [13] Urban ecosystems / green infrastructure Street trees, rain gardens, green roofs; urban birds & insects Stormwater retention & water quality; urban heat mitigation; amenity Washington, DC Stormwater Retention Credit market [14]; Philadelphia stormwater grants/credits [15] Marine & coastal (reefs, seagrass) Coral reefs; seagrasses; herbivorous fish; sea turtles Tourism & recreation; shoreline protection; sustainable fisheries Bonaire National Marine Park user-fee system [16] Table 2. PES schemes involving microbial outcomes: evaluation axes, microbial focus, and limitations. FIB: fecal indicator bacteria Scheme / Region Outcome metrics Microbial focus Monitoring methods Payment linkage Limitations NYC Catskill–Delaware watershed (USA) [5] Drinking-water safety, FAD maintenance FIB / pathogens ( E. coli , Giardia , Cryptosporidium ) Regulatory monitoring, land management compliance Payments for upstream land management Microbial diversity and functions not included Bolivia “Watershared” program [17] Reduction in E. coli (validated by RCT) FIB only ( E. coli ) Water sampling in RCT design Payments to upstream landholders Diversity and functions excluded Water Funds in Latin America (e.g., Quito FONAG, FORAGUA) [10] Water quality and quantity FIB / general microbial contamination Routine water monitoring User contributions to upstream conservation Diversity rarely included Urban GSI (constructed wetlands, bioretention, rain gardens) [19,20] FIB log reduction at outflow FIB indicators ( E. coli , Enterococci) On-site sampling, performance evaluation Stormwater fee credits, grants High variability; diversity remains supplementary Supplementary Material File (260117_pes_manuscript_clean_figures and tables.pdf) Download 630.60 KB Information & Authors Information Version history V1 Version 1 21 January 2026 Peer review timeline Published npj Biodiversity Version of Record 18 May 2026 Published Copyright This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License Keywords microbial diversity nature positive payments for ecosystem services public health Authors Affiliations Kohei Ito 0000-0001-8267-4495 [email protected] View all articles by this author Honami Ando 0009-0008-1757-6117 View all articles by this author Hiroshi Honda 0000-0002-2936-2617 [email protected] Honda Biotech. Laboratory University of Yamanashi View all articles by this author Metrics & Citations Metrics Article Usage 296 views 104 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Kohei Ito, Honami Ando, Hiroshi Honda. Microbial Diversity as the Next Frontier of Payments for Ecosystem Services in Nature-Positive Finance. Authorea . 21 January 2026. DOI: https://doi.org/10.22541/au.176901865.58628984/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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