The research, published in the journal Metabarcoding and Metagenomics, focused on the short-finned pilot whale (Globicephala macrorhynchus), a highly social species with a global distribution and a well-documented propensity for mass strandings. Respiratory tract infections rank among the leading causes of death in cetaceans, making the microbial community of the airways a potentially powerful biomarker of respiratory health. Yet most existing data on cetacean-associated microbes come from captive, stranded, sick or injured individuals, which cannot be considered representative of healthy free-ranging populations. The new study set out to fill that gap by sampling wild whales in their natural environment.

Between September and October 2018, researchers conducted at-sea monitoring campaigns in the southern waters of Madeira Island, Portugal. Using a PERFORMAgene PG-100 swab collection kit attached to a five-metre extendable aluminium pole, the team positioned the sampling device roughly 40 to 50 centimetres above the blowhole of surfacing whales to capture droplets from the exhaled plume. The animals were approached slowly from an eight-metre rigid inflatable boat under permits from the Instituto de Florestas e Conservação da Natureza IP-RAM. In total, twelve blow samples were collected across six sampling events, nine from individual animals and three from pools of individuals within the same group. Photographic identification against Madeira’s catalogue of the species confirmed that the nine individual samples corresponded to seven distinct animals, two of which were sampled on separate occasions.

A notable methodological first accompanied the sampling: the PERFORMAgene kit, previously used for livestock and pets, had never been reported in the literature for collecting blow from free-ranging cetaceans. The kit offers practical advantages for fieldwork, stabilising DNA samples for up to a year at room temperature, which provides safe flexibility during transportation and storage. Although DNA concentrations extracted from the swabs were low, the method proved suitable for downstream metabarcoding analysis. The researchers also observed no evident changes in the whales’ swimming patterns or behaviour during sampling, suggesting the procedure causes minimal distress, though they recommend future studies formally monitor behavioural responses alongside collection.

The core of the study was a rigorous comparison of two primer sets targeting different hypervariable regions of the 16S rRNA gene, the standard molecular marker for characterising bacterial and archaeal communities. The V3-V4 region, amplified with primers 341F and 806R, had been used in previous cetacean blow studies, while the V4-V5 region, amplified with primers 515F-Y/926R, is currently recommended by the Earth Microbiome Project for targeting marine microbes. By applying both primer sets to the same twelve samples, using identical DNA extraction, library preparation, sequencing on an Illumina MiSeq platform and bioinformatic processing through the DADA2 pipeline, the researchers eliminated technical biases that typically confound such comparisons.

Sequencing yielded a total of 685,692 reads for the V3-V4 dataset and 862,763 reads for the V4-V5 dataset. After quality filtering, the final output comprised 415,340 sequences assigned to 2,764 Amplicon Sequence Variants (ASVs) in the V3-V4 dataset and 417,733 sequences assigned to 3,665 ASVs in the V4-V5 dataset. ASVs resolve sequences to the level of a single nucleotide difference, offering finer taxonomic resolution than traditional operational taxonomic units. Taxonomic classification was performed with a Naïve Bayes classifier against the curated SILVA database, and undesirable lineages such as chloroplast, eukaryote and mitochondrial sequences were excluded from further analysis.

The comparison revealed striking differences between the two primer sets. Alpha diversity metrics varied significantly: the V4-V5 dataset captured roughly 32 percent more bacterial ASVs, with higher values for the Observed and Chao1 richness measures, while the V3-V4 dataset produced higher Shannon and Inverse Simpson diversity values. A statistical test using the Wilcoxon Signed-Rank procedure confirmed significant differences between primer sets for most measures. Beta diversity analysis, based on Bray-Curtis dissimilarity and visualised through non-metric multidimensional scaling, showed that samples clustered according to the primer set used. A PERMANOVA test found that the primer choice explained approximately 25 percent of the variation in prokaryotic community distribution, a substantial technical effect that researchers designing future cetacean microbiome studies cannot afford to ignore.

Despite these differences, all blow samples shared a core microbiota composed of four dominant phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. This aligns with previous findings in bottlenose dolphins, humpback whales and other cetacean species, where Proteobacteria is consistently highly abundant. At the genus level, the V3-V4 dataset was dominated by Pseudomonas, while the V4-V5 dataset was dominated by Cutibacterium, a genus typical of nasal microbiota. The oceanic bacterium Prochlorococcus, one of the most abundant bacteria in the sea, was detected in both datasets and is probably a seawater-associated organism within the blow. The researchers noted that control water samples were not taken in this study but consider them extremely important for future work to disentangle the influence of ambient seawater on the detected microbial composition.

Perhaps the most intriguing finding concerns sociality. In the V4-V5 dataset, individuals that were travelling together when sampled, such as the pairs Gma_2 and Gma_3 or Gma_4 and Gma_5, clustered together in the community analyses, a pattern not observed with the V3-V4 primers. This supports the hypothesis that social behaviour shapes the respiratory microbiome in cetaceans. Short-finned pilot whales live in matrilineal groups with long-lasting relationships, and behaviours such as surfacing and breathing near each other or feeding cooperatively could facilitate microbial transfer between individuals. Previous work on whale species has detected a positive correlation between sociality and microbial diversity in blow, and the new results strengthen the idea that social complexity influences microbiome composition in the respiratory tract of these marine mammals.

The study also carries implications for disease surveillance. Four of the most abundant genera detected in both datasets, Pseudomonas, Flavobacterium, Rhodococcus and Sphingomonas, are potential pathogenic genera commonly related to pulmonary infections, although their presence does not necessarily indicate disease since not all members of these taxa are pathogenic. The V4-V5 primers proved particularly valuable for detecting the rare microbial biosphere, the low-abundance taxa that could include organisms with pathogenic potential, and for capturing the core microbiome more consistently. The authors conclude that primer selection should depend on the analytical goal: V3-V4 performs better for capturing diversity present at higher relative abundance, while V4-V5 is preferable for identifying unique ASVs and rare taxa. A combination of both primer sets may ultimately provide the most robust characterisation of the blow microbiome. With further optimisation of sampling protocols and integration with complementary health measures such as photogrammetry-based body condition assessment, whale breath could become a routine biomarker for monitoring the physiological state of airways in free-ranging cetacean populations worldwide.

Subject of Research: Respiratory microbiome characterisation of free-ranging short-finned pilot whales using blow samples and 16S rRNA metabarcoding

Article Title: Hidden in the blow – a matrix to characterise cetaceans’ respiratory microbiome: short-finned pilot whale as case study

Article References: Santos, B., Afonso, L., Alves, F., Dinis, A., Ferreira, R., Correia, A. M., Valente, R., Gil, Á., Castro, L. F. C., Sousa-Pinto, I., Rosso, M., Centelleghe, C., Mazzariol, S., Magalhães, C., & Tomasino, M. P. (2024). Hidden in the blow – a matrix to characterise cetaceans’ respiratory microbiome: short-finned pilot whale as case study. Metabarcoding and Metagenomics, 8, Article e121060. https://doi.org/10.3897/mbmg.8.121060

Image Credits: AI Generated

DOI: 10.3897/mbmg.8.121060

Keywords: cetaceans, short-finned pilot whale, blow microbiome, respiratory health, 16S rRNA metabarcoding, Madeira Island, exhaled breath condensate, marine mammals, microbiome, non-invasive sampling, rare biosphere, sociality

The research, led by Yuguang Wang, Longqi Xu and colleagues at Central South University in Changsha, China, examined a river system impacted by acid mine drainage, sampling both the flowing water and the underlying sediments along the contamination gradient. Rather than treating the microbial community as a single entity, the team split it into three compartments: the whole prokaryotic community, the abundant taxa that dominate biomass, and the rare taxa that linger at vanishingly low concentrations. This partitioning matters because ecologists have increasingly recognized that the rare biosphere, the enormous reservoir of low-abundance microorganisms, may behave according to entirely different rules than its abundant counterparts.

The first major finding concerns spatial structure. In sediment habitats, diversity and composition of the whole community and of abundant taxa changed significantly along the river, tracking the geochemical shifts imposed by the drainage. The relative abundances of Gammaproteobacteria and Betaproteobacteria, classes that often thrive in the most acidic, metal-rich zones near the pollution source, declined progressively downstream. In their place, Alphaproteobacteria and members of the phylum Acidobacteriota increased, suggesting a succession of acid-tolerant specialists as conditions gradually moderated. This directional turnover mirrors patterns documented in other acid mine drainage systems across southern China, where environmental heterogeneity and geographic isolation jointly sculpt microbial succession.

Water habitats told a strikingly different story. Unlike the sediments, the water column showed no significant spatial variation in community diversity or composition for the whole community or abundant taxa. Instead, the water was characterized by genera such as Acidovorax and Acidocella, acidophilic bacteria well adapted to the chemically uniform, continuously mixed conditions of the river channel. The contrast between sediment and water underscores a fundamental principle of microbial biogeography: habitat type can override pollution gradients in determining which ecological forces dominate. Sediments, with their layered chemistry, particle surfaces and pore waters, create microenvironments where deterministic filtering by environmental conditions leaves a clear spatial fingerprint. The well-mixed water column, by contrast, homogenizes conditions and appears to erase much of that spatial signal.

To understand how these communities came to be, the researchers turned to the conceptual machinery of community assembly theory. Ecologists distinguish between deterministic processes, in which environmental selection favors organisms with suitable traits, and stochastic processes, in which random dispersal, ecological drift and historical contingency shape which species end up where. Using null model analysis, which compares observed community turnover against what would be expected by chance, the team quantified the relative contributions of heterogeneous selection, homogeneous selection, dispersal limitation, dispersal and undominated processes.

The verdict was clear: stochasticity rules, especially for the rare biosphere. Dispersal limitation and undominated processes, a category capturing the combined effects of weak selection and weak dispersal, generally dominated community assembly, and this was most pronounced for rare taxa. The alpha diversity of rare taxa showed no significant correlation with spatial distance in either sediments or water, indicating that these low-abundance organisms are distributed in ways that defy simple geographic or environmental gradients. For the abundant taxa and the whole community in sediments, however, deterministic processes, both heterogeneous and homogeneous selection, still played a role that could not be ignored. In other words, the dominant players in the sediment are filtered by the harsh chemistry of acid mine drainage, while the rare players arrive and persist largely by chance.

Perhaps the most provocative result came from the co-occurrence network analysis. When the researchers mapped which taxa appear together across samples, constructing a network of potential ecological interactions, they found that rare taxa occupied important topological positions. These are the nodes that connect distant parts of the network, acting as potential keystone species whose removal could restructure the entire community. The finding resonates with a growing body of evidence that the rare biosphere punches far above its numerical weight. Studies in fertilized soils, acidic soils and other ecosystems have shown that rare microorganisms can be major drivers of ecosystem multifunctionality, and theoretical work has argued that the rare biosphere may serve as a dormant seed bank that resuscitates during pulses of ecosystem activity.

Why would rare taxa occupy such influential positions in a system as extreme as an acid mine drainage river? One possibility is that rarity itself is a strategy. Many rare organisms are specialists with narrow environmental tolerances, active only in fleeting favorable microenvironments. In a chemically heterogeneous system, these specialists may broker interactions between abundant generalists, facilitating the transfer of metabolites such as organic acids, iron species or sulfur intermediates across guild boundaries. Another possibility is that network edges involving rare taxa reflect shared responses to fine-scale environmental variation that abundant taxa, buffered by their sheer numbers, do not experience. Either way, the result challenges the practice of focusing monitoring and remediation assessments solely on dominant organisms.

The study also carries practical implications for managing mine-polluted rivers. Acid mine drainage is a global problem, contaminating thousands of kilometers of waterways with acidity, iron, aluminum, manganese and toxic metalloids. Natural attenuation, the gradual reduction of pollutant loads by intrinsic physical, chemical and biological processes, depends heavily on microbial activity, particularly sulfate-reducing bacteria and iron-cycling organisms that can immobilize metals as sulfides and oxides. If rare taxa hold key positions in the interaction networks that underpin these functions, then perturbations that further reduce rare diversity, such as episodic acid pulses or engineering interventions that disturb sediments, could have outsized and unpredictable consequences for the river’s capacity to heal itself.

The research also refines how scientists should read microbial communities as pollution indicators. Previous work on copper-contaminated river sediments suggested that abundant taxa are more sensitive bio-indicators than rare ones, and the present study partly supports that view: abundant taxa in sediments responded strongly and predictably to the spatial environmental gradient. But the new findings add nuance. Abundant taxa may tell you where the pollution is, while rare taxa may tell you how the ecosystem is wired. Effective ecological evaluation of acid mine drainage impact, the authors suggest, requires tracking both compartments and recognizing that they are assembled by different forces.

Methodologically, the study exemplifies the current toolkit of microbial ecology. High-throughput amplicon sequencing of the 16S ribosomal RNA gene, processed through rigorous quality control and denoising pipelines, provided the taxonomic inventory. Environmental variables measured alongside the biological samples allowed the team to link community patterns to geochemistry. Null models converted patterns into process, and network analysis converted co-occurrence into hypotheses about interaction. This integrated approach is rapidly becoming the standard for disentangling the ecology of complex microbial systems, from Antarctic lakes to tropical ocean waters to contaminated rivers.

The broader message is one of humility about where ecological power resides. In a river poisoned by acid mine drainage, the visible story, the dominant Gammaproteobacteria near the source, the Acidobacteriota downstream, the Acidovorax in the water, is written by environmental selection and reads clearly along the pollution gradient. But the hidden story, the one told by dispersal limitation, random drift and the quiet influence of organisms too scarce to notice, may be just as important. As the rare biosphere continues to reveal itself across ecosystems, ecologists are learning that in microbial worlds, less may indeed be more, and the smallest players may hold the strings of the entire system.

Subject of Research: Microbial community assembly of abundant and rare prokaryotic taxa in an acid mine drainage-impacted river system

Article Title: Distinct ecological patterns of abundant and rare prokaryotic taxa across sediment and water habitats in an acid mine drainage-impacted river system

Article References: Wang, Y., Xu, L., Ai, C., Chen, Z., Zhou, H., & Cheng, H. (2026). Distinct ecological patterns of abundant and rare prokaryotic taxa across sediment and water habitats in an acid mine drainage-impacted river system. Environmental Geochemistry and Health, 48(15), Article 619. https://doi.org/10.1007/s10653-026-03523-y

Image Credits: AI Generated

DOI: 10.1007/s10653-026-03523-y

Keywords: acid mine drainage, rare biosphere, microbial ecology, community assembly, co-occurrence network, prokaryotes, sediment microbiology, river pollution, heavy metals, stochastic processes, biogeography, environmental microbiology

The study, published in the journal Ocean Microbiology, analyzed 726 samples of 16S rRNA gene amplicons collected between 2011 and 2023, detecting more than 67,000 distinct prokaryotic amplicon sequence variants, or ASVs. The team, led by Carina Bunse of Linnaeus University and the University of Gothenburg together with Jarone Pinhassi and colleagues, split each sample into two size fractions: particle-associated prokaryotes larger than 3 micrometers, and free-living cells in the 0.2 to 3 micrometer range. This dual-fraction approach, sustained over more than a decade, is rare in oceanography and allowed the researchers to ask questions that shorter studies simply cannot answer.

The sampling site itself experiences dramatic seasonal forcing. Winter water temperatures drop below 5 degrees Celsius while inorganic nutrients accumulate to concentrations of 2 to 3 micromolar nitrate plus nitrite and up to 1 micromolar phosphate. By summer, temperatures climb to 18 degrees or higher, and nutrients are stripped to near detection limits. Two major phytoplankton blooms punctuate the year, one typically in April dominated by dinoflagellates and diatoms, and a cyanobacterial bloom in July and August. Prokaryotic cell counts swing roughly six-fold, from about half a million cells per milliliter in winter to more than three million in summer.

One of the study’s clearest findings concerns biodiversity. Particle-associated communities consistently harbored higher diversity than free-living ones, with estimated and observed richness significantly elevated in the particle fraction across all seasons, peaking in winter. This makes ecological sense: marine particles, whether aggregates of living and dead plankton, fecal pellets, or condensed organic material, offer a patchwork of microscopic habitats, each with its own chemistry and resources. Free-living seawater, by contrast, selects for streamlined cells adapted to a more homogeneous environment. Yet the evenness of the communities, measured by Shannon and inverse Simpson indices, differed between fractions only in winter, suggesting that while particles host more species, the balance of abundance remains broadly similar.

The researchers went further, using a permutation-based particle-association niche index to determine which taxa genuinely prefer particles and which prefer open water. The results revealed remarkable fine-scale specialization. Among the Bacteroidia and Gammaproteobacteria, most families showed strong particle association, including Alteromonadaceae, Pseudomonadaceae, and Shewanellaceae. Among the Alphaproteobacteria, families split roughly evenly, with Rhizobiaceae and Caulobacteraceae favoring particles while Rhodospirillaceae and the famously abundant Pelagibacteraceae favored the free-living fraction. Most strikingly, some families such as Flavobacteriaceae, Burkholderiaceae, and Rhodobacteraceae contained species spread across the entire spectrum, meaning that even within a single family, closely related organisms have carved out opposite lifestyles.

The filamentous cyanobacteria provided a natural test case. Genera like Dolichospermum, Nodularia, and Aphanizomenon form the Baltic Sea’s notorious summer blooms, thriving on nitrogen limitation and residual phosphorus. In the dataset, Cyanobacteriia dominated the particle fraction in summer, sometimes exceeding 90 percent of relative abundance, while contributing at most around 30 percent to the free-living fraction, largely because their filaments are physically excluded from the smaller filter. Non-filamentous cyanobacterial families, by contrast, showed low particle-association indices, confirming that the fractionation captures real biology rather than an artifact of filtration.

Perhaps the most unexpected finding involves the rare biosphere. Most ASVs in the dataset were consistently rare, with mean relative abundances below 0.7 percent. But the abundant taxa, the so-called core species that appear in high numbers every year, turned out to be surprisingly ephemeral. A majority of the 50 most abundant ASVs in each fraction collapsed into the rare biosphere for extended stretches of the year, sometimes falling below detection entirely, before rebounding in their characteristic season. Recruitment from the rare biosphere, previously viewed as an occasional event following disturbance, appears here to be an annual routine for most dominant taxa in this strongly seasonal environment.

The dataset also captured rare microbes responding to dramatic events. Campylobacteria, formerly known as Epsilonproteobacteria, normally inhabit the oxic-anoxic interface in deeper Baltic waters. Yet in the winters of 2011/12 and 2014/15, coinciding with major North Sea inflow events that pushed saline, oxygenated water into the Baltic’s deep basins, a Sulfurimonas ASV surged to relative abundances exceeding 80 percent in surface waters in December 2011. These episodic blooms of typically deep-water specialists offer a microbial fingerprint of large-scale oceanographic disturbances, lingering for months before the taxa retreated back into rarity.

The centerpiece of the study, however, is the demonstration of direction-dependent dynamics, a phenomenon ecologists call hysteresis. Using generalized additive models that compared a single temperature-abundance relationship against models allowing separate smooths for warming and cooling phases, the researchers found that most co-occurring taxon clusters behaved differently depending on the direction of environmental change. One free-living cluster dominated by Bacteroidia reached roughly 50 percent relative abundance at 7 degrees Celsius in spring but only about 15 percent at the same temperature in autumn. Another cluster, rich in Acidimicrobiia and Actinomycetes, accounted for more than 40 percent of the community at 10 degrees in autumn but a mere 5 percent at 10 degrees in spring. The same held for day length: one cluster exceeded 60 percent abundance at 15 hours of daylight in spring but contributed less than 10 percent at 15 hours in fall.

What does this mean for how we understand the ocean’s microbial engines? Temperature undeniably shapes microbial metabolism, and day length defines the seasonal calendar at any latitude. But the study’s authors argue that neither variable directly determines community composition. Instead, the identity of the microbes at any moment reflects the community’s history, the direction of environmental change, the quantity and quality of organic and inorganic nutrients, and a web of biotic interactions with phytoplankton, grazers, and viruses. Spring waters carry fresh labile organic matter from the phytoplankton bloom; autumn waters carry a different cocktail of substrates after a summer of production and degradation. The microbes respond to this context, not just to the thermometer. Given that seasonal shifts in dominant microorganisms ripple through marine food webs and biogeochemical cycles, the finding suggests that climate-driven warming may alter ecosystems in ways that simple temperature correlations cannot predict. For a brackish inland sea already stressed by eutrophication and hypoxia, that is a sobering message, and one that only long-term, high-frequency, size-fractionated time series like this one could have delivered.

Subject of Research: Seasonal succession and direction-dependent dynamics of particle-associated and free-living prokaryotic communities in the Baltic Sea

Article Title: Comparable temperatures but different microbiomes: long-term time series exposes seasonally divergent Baltic Sea prokaryotic communities

Article References: Bunse, C., Farnelid, H., Lindehoff, E., Martínez-García, S., Fridolfsson, E., Di Leo, D., Martínez, C. P., Pontiller, B., Lindh, M. V., Sjöstedt, J., Lundin, D., Legrand, C., & Pinhassi, J. (2026). Comparable temperatures but different microbiomes: long-term time series exposes seasonally divergent Baltic Sea prokaryotic communities. Ocean Microbiology, 2(1), Article 5. https://doi.org/10.1186/s44375-026-00011-7

Image Credits: AI Generated

DOI: 10.1186/s44375-026-00011-7

Keywords: Baltic Sea, prokaryoplankton, microbiome, seasonal succession, time series, rare biosphere, hysteresis, particle-associated bacteria, free-living bacteria, cyanobacteria, 16S rRNA, marine microbial ecology

The review, authored by Debarshi Dasgupta of the Indian Agricultural Research Institute and North Dakota State University, synthesizes soil microbial ecology across five interconnected themes: the energy dynamics of soil food webs, rhizosphere plant-microbe interactions, the ecology of arbuscular mycorrhizal fungi, the biological regulation of nitrogen cycling, and the translation of soil biodiversity into ecosystem services. Its central contention is provocative: ecological theory already provides a sufficient conceptual basis for redesigning agroecosystems around microbial functionalities. The timing could hardly be more urgent. Close to one-third of the world’s soils are already moderately to severely degraded, and with the global population projected to reach approximately 9.7 billion by 2050, food systems must maintain or expand productivity precisely when the biological foundations of that capacity are in measurable decline.

One of the review’s most striking arguments concerns the architecture of the soil food web itself. Far from being an undifferentiated cloud of activity, the decomposer community is organized around two dominant energy channels that are functionally divergent in profound ways. The bacterial channel is fast: it thrives on labile, low carbon-to-nitrogen substrates such as fresh root exudates, drives rapid nutrient turnover, and dominates in tilled, heavily fertilized systems. The fungal channel operates more slowly, sustained by recalcitrant materials like lignin and cellulose, and produces stable compounds such as glomalin and melanin that bind soil particles into the macroaggregates essential for long-term carbon sequestration. Because fungal hyphae physically enmesh mineral particles, fungal-dominated communities build soil structure in ways bacterial communities cannot match.

The practical stakes of this distinction are illustrated by a comparative study of 60 grassland and arable sites across Europe, cited in the review, which found that the ratio of fungal to bacterial biomass predicted soil carbon storage and nitrogen retention more strongly than any single chemical property of the soil. Communities with higher fungal dominance were also significantly more resistant to drought-induced reductions in carbon mineralization. This identifies a genuine leverage point for farmers: the practices that promote fungal energy channels, including reduced tillage, continuous soil cover, high carbon-to-nitrogen organic inputs and diverse rotations, are precisely the practices that promote carbon sequestration and drought resilience. Long-term studies consistently show that intensive cultivation shifts communities from fungal toward bacterial dominance, with measurable consequences for soil carbon stocks and structural stability.

The review also highlights the understated role of grazing within the soil food web. Protozoa and nematodes that consume bacterial and fungal biomass excrete excess nitrogen as ammonium at every trophic transfer, effectively mineralizing organic nitrogen at each step of the food chain, a phenomenon known as the microbial loop. Because microbial populations exhibit logistic growth, moderate grazing pressure actually stimulates rather than suppresses microbial productivity, a principle called grazing optimization. From the plant’s perspective, the predatory community is therefore not merely a competitor for microbial biomass but a driver of the very nitrogen mineralization that feeds crop growth. Notably, a recent long-term field experiment manipulating nematode predation directly found that nematode addition increased multitrophic energy fluxes by between 5.9 and 169.4 percent, translating into higher soil multifunctionality, increased grain yield and greater root biomass. Conversely, a biocide application in a long-term corn-soybean system proved the most effective treatment at collapsing the soil’s natural suppressiveness to the soybean cyst nematode, a major yield-limiting pathogen, demonstrating that the biological community itself, not merely physical disturbance, confers disease suppression.

Among the most uncomfortable findings in soil ecology is how slowly these communities recover once simplified. Chronosequence studies show that while the first few years of transition to reduced tillage bring modest improvements in microbial biomass, the full reorganization of food web structure, including the recovery of fungal channels and the return of predatory arthropods and earthworms, can take a decade or more. A long-term experiment in the southern Coastal Plain of Georgia, tracking cotton fields from 4 to 25 years under no-till management, found that only the oldest fields had accumulated organismal abundance and species richness approaching undisturbed reference sites. The implication, the review stresses, is not an argument against ecological management but an argument for starting immediately, because ecological benefits compound slowly and ecological debts are repaid on the same slow timescale.

The rhizosphere, the narrow zone of soil under the direct influence of plant roots, emerges as agriculture’s most productive microhabitat. Microbial populations there are typically 10 to 100 times higher than in bulk soil, sustained by the continuous input of root-derived carbon. Root exudates act as structured chemical signals that recruit specific microbial partners: malic acid secreted under phosphorus stress recruits biocontrol strains of Bacillus subtilis, organic acids such as citrate and oxalate solubilize phosphorus bound to iron and aluminum, and legume flavonoids initiate the molecular dialogue leading to rhizobial nodule formation. Plant growth-promoting rhizobacteria, long heralded as a biotechnological solution, show routinely dramatic effects in glasshouse experiments, but field meta-analyses reveal positive mean effects with standard deviations comparable to the means themselves, a variability rooted in the difficulty of establishing an inoculated strain against locally adapted indigenous communities. Encouragingly, a synthesis of 52 studies found inoculation increased root mass by 35 percent and reproductive yield by 19 percent under well-watered conditions, with effects growing even larger under drought.

The review devotes particular attention to arbuscular mycorrhizal fungi, the most ancient and widespread mutualism in terrestrial plant nutrition, dating roughly 450 million years to the Ordovician colonization of land. Today approximately 80 percent of land plant species, including the majority of staple food crops, maintain the partnership, in which fungi receive 4 to 20 percent of plant photosynthate in exchange for extending the root’s absorptive reach into soil pores too narrow for root hairs. Under moderate phosphorus availability, mycorrhizal plants can derive 70 to 80 percent of their phosphorus uptake through the fungal pathway. Yet the symbiosis is not unconditionally mutualistic: in high-phosphorus fertilized soils, fungi may colonize roots and draw plant carbon without delivering commensurate benefit, tipping the relationship toward parasitism. A single tillage event can reduce mycorrhizal colonization of the next crop by 30 to 50 percent in the first weeks after planting, and bare fallows can cause declines persisting for years. The prescribed remedy is a coherent conservation toolkit: reduced tillage, mycorrhizal cover crops during fallows, moderated phosphorus inputs and diverse rotations.

On nitrogen, the review frames the global cycle as a microbial achievement disrupted by twentieth-century chemistry. An estimated 40 to 50 percent of synthetic fertilizer nitrogen is not taken up by crops, instead leaching into groundwater, escaping as nitrous oxide, a greenhouse gas roughly 265 times more potent than carbon dioxide over a century, or cascading into eutrophication. Biological nitrogen fixation by legume symbionts contributes an estimated 40 to 60 million tonnes of nitrogen globally per year, with individual legume crops fixing between 100 and 300 kilograms per hectare per season under favorable conditions. The central design challenge is synchrony: aligning biological mineralization with crop demand through residue quality management and input timing. Evidence from sub-Saharan Africa underscores the potential, with a meta-analysis of 94 studies finding that legume integration often doubled or tripled yields at low-producing sites, and adding half the recommended mineral fertilizer rate increased yields a further 25 percent over legumes alone.

Ultimately, the review contends that soil biodiversity functions as ecological insurance. Rare microbial taxa, those present at low relative abundances, account for a disproportionate share of key processes including nitrogen fixation, phosphorus mineralization and the decomposition of recalcitrant compounds, and their selective erosion under intensification carries functional consequences far beyond what numerical abundance suggests. The biological capital of agricultural soils has been systematically undervalued, underprotected and underinvested in for the better part of a century, the author concludes, and the consequences are now materializing in ways that directly threaten long-term productive capacity. The understanding needed to begin treating the soil microbiome as a foundational agricultural resource, as essential as seeds and water, already exists. What remains, the paper argues, is the will to use it.

Subject of Research: The role of belowground microbial communities in sustainable agroecosystem management

Article Title: Belowground microbial stewardship underpins sustainable agroecosystem management

Article References: Dasgupta, D. (2026). Belowground microbial stewardship underpins sustainable agroecosystem management. Discover Soil, 3(1), Article 162. https://doi.org/10.1007/s44378-026-00323-9

Image Credits: AI Generated

DOI: 10.1007/s44378-026-00323-9

Keywords: soil microbiome, soil food web, arbuscular mycorrhizal fungi, nitrogen cycling, rhizosphere, soil biodiversity, conservation agriculture, ecosystem services, soil organic matter, plant growth-promoting rhizobacteria, agroecosystem sustainability, rare biosphere

A new landmark editorial launching Ocean Microbiology, an open-access journal dedicated to marine and aquatic microorganisms, argues that the field stands at a unique crossroads. The publication, authored by Ramiro Logares of the Institute of Marine Sciences in Barcelona, describes a golden age of marine microbial research, powered by an extraordinary convergence of technologies that have transformed what scientists can see and measure. Over the past two decades, high-throughput DNA sequencing, high-resolution imaging, microfluidics and single-cell technologies, advanced bioinformatics, autonomous monitoring systems, predictive modeling and new theoretical frameworks have together revealed the diversity and complexity of ocean microbes at unprecedented scales, opening windows onto a world that was almost entirely hidden a generation ago.

The technical achievements of this era have been stunning in their scope. Large-scale sequencing campaigns have uncovered millions of novel microbial genes, dramatically expanding understanding of the metabolic potential harbored in ocean waters—genes that hint at undiscovered biochemistries operating in every liter of seawater. Surveys of plankton across ocean basins have exposed the existence of a vast ‘rare biosphere,’ an enormous collection of low-abundance microbial taxa that nonetheless perform ecologically relevant roles in nutrient cycling and energy flow. Completely new lineages of microorganisms have been described, some of which are forcing biologists to redraw portions of the tree of life itself. And beneath the boundaries of species definitions, researchers are detecting a large but still overlooked diversity within microbial populations, revealing evolutionary dynamics occurring at fine genetic scales that classical methods could never resolve.

Equally transformative has been the growing appreciation of microbial ecology as a web of interactions rather than a roster of species. Scientists are now characterizing the myriad ecological relationships that sustain marine food webs and underpin ocean ecosystem functioning, including newly mapped interaction networks, syntrophic associations in which different microbes cooperate metabolically to complete chemical transformations neither could achieve alone, and symbioses that bind microorganisms to hosts ranging from corals to fish larvae. These interactions play key roles in ecosystem functioning and nutrient cycling, and their disruption—by warming, acidification or pollution—could cascade through marine ecosystems in ways scientists are only beginning to anticipate. The editorial emphasizes that unveiling these interaction networks is one of the central tasks facing the next generation of marine microbiologists.

But the same editorial does not celebrate unreservedly. It arrives at a moment when accelerating climate change, including ocean warming and acidification, together with other anthropogenic pressures such as pollution, is impacting marine ecosystems at an unprecedented pace. Because microbes mediate the biogeochemical reactions that determine how much carbon the ocean absorbs, how efficiently nutrients are recycled, and how productive fisheries will be, understanding how microbial communities respond and adapt to these pressures has become a matter of global urgency. The convergence of unprecedented technological capability with unprecedented environmental stress, the editorial argues, creates both opportunities and responsibilities for the marine microbiology community worldwide.

The technical toolkit for meeting that responsibility is maturing rapidly. Long-term ocean observatory programs now monitor microbial communities across years and decades, producing time series that can distinguish genuine trends in microbial abundance and composition from natural seasonal and interannual variability. When coupled with new predictive models—drawing on machine learning, ecosystem modeling and increasingly sophisticated representations of microbial metabolism—these observatories are expected to yield essential insights into how the ocean microbiome may be changing over time, and into its resistance, resilience, or potential fragility in the face of multiple simultaneous stressors. Such forecasting capability is exactly what policymakers and ocean managers will need as climate impacts intensify through the middle of the century.

Timing matters in another sense as well. The editorial notes that as the United Nations Decade of Ocean Science for Sustainable Development, running from 2021 to 2030, reaches its midpoint, advancing understanding of microbial responses to global change has become essential for forecasting the future health of the ocean. International frameworks like the Ocean Decade have elevated the microbiome from a specialist concern to a central pillar of ocean sustainability science, reflecting the recognition that no meaningful model of the future ocean can be built without representing the microbial processes that regulate it. The launch of a dedicated, open-access venue for the field is framed as part of this broader institutional shift toward treating ocean microbes as infrastructure of the biosphere.

The new journal is explicitly designed around the interdisciplinary character of modern marine microbiology. The editorial stresses that the field requires integration across scales: from molecular mechanisms inside single cells to ecosystem processes spanning whole basins, from tightly controlled laboratory experiments to global ocean observations gathered by ships, floats and satellites, and from micro- to macroecological perspectives. Accordingly, the journal welcomes research spanning microbial diversity, genomics and evolution; biogeochemical cycles and microbial metabolism; host–microbe interactions; microbial responses to global change; marine biotechnology and applied microbiology, including so-called blue biotechnology and nature-based solutions to societal challenges; methodological and theoretical advances; and microbial oceanography, including studies of large-scale ecological patterns across the ocean.

The applied dimension of the field deserves particular attention, because the same microbial capabilities that run the planet’s cycles also represent a resource for human society. Marine microbes are a reservoir of enzymes, natural products and metabolic pathways with potential uses in medicine, industry and environmental remediation. Nature-based solutions inspired by microbial processes—harnessing communities that degrade pollutants, cycle nutrients in aquaculture systems or buffer coastal ecosystems against climate impacts—form a growing frontier where fundamental ocean microbiology translates directly into tools for sustainability. The editorial signals that such translational research will sit alongside discovery-driven science in the new journal’s scope, reflecting the field’s expanding societal relevance.

The invitation to the community is broad. The editorial calls on marine microbiologists across all career stages, in every region of the world, to submit their research, contribute as reviewers and help shape a publication intended not merely to document progress but to influence the future direction of marine and aquatic microbial science. As Logares writes in closing, sitting by the ocean one wonders what new secrets it will unveil in the coming years. Given the pace of discovery, the accelerating pressures of global change, and the sheer scale of the microbial world that remains unexplored, that question may well define ocean science for the rest of the decade.

Subject of Research: The ocean microbiome and its role in Earth system functioning under global change

Article Title: The ocean microbiome on a changing planet

Article References: Logares, R. (2025). The ocean microbiome on a changing planet. Ocean Microbiology, 1(1), Article 1. https://doi.org/10.1186/s44375-025-00004-y

Image Credits: AI Generated

DOI: 10.1186/s44375-025-00004-y

Keywords: ocean microbiome, marine microbiology, climate change, biogeochemical cycles, rare biosphere, microbial genomics, ocean warming, ocean acidification, symbiosis, blue biotechnology, microbial ecology, Ocean Decade