The global microbiome sequencing services market is experiencing robust growth, driven by the increasing understanding of the microbiome's role in human health and disease. Advancements in sequencing technologies, such as next-generation sequencing (NGS), are significantly reducing costs and increasing throughput, making microbiome analysis more accessible to researchers, pharmaceutical companies, and healthcare providers. The pharmaceutical and biotech sectors are major drivers, leveraging microbiome sequencing to identify novel drug targets and develop personalized therapies for various conditions, including gastrointestinal disorders, autoimmune diseases, and even cancer. Academic institutions are also contributing significantly to the market's expansion through fundamental research and the development of innovative analytical tools. Regulatory support and increased funding for microbiome research further bolster market growth. While the market is currently dominated by sequencing by synthesis (SBS) methods, other technologies like sequencing by ligation are gaining traction due to their potential for specific applications. The market exhibits significant regional variations, with North America and Europe currently holding the largest market share due to the presence of well-established research infrastructure and a high concentration of key players. However, the Asia-Pacific region is projected to witness the fastest growth in the coming years, driven by increasing healthcare spending and rising awareness of microbiome-related health issues. Challenges remain, primarily related to data analysis and interpretation. The sheer volume of data generated by microbiome sequencing requires sophisticated bioinformatics tools and expertise for accurate and meaningful insights. Furthermore, standardization of protocols and data analysis pipelines is crucial for ensuring reproducibility and comparability of results across different studies and laboratories. Despite these hurdles, the market is poised for sustained growth, propelled by ongoing technological innovation, the increasing adoption of microbiome-based diagnostics and therapeutics, and a growing understanding of the complex interplay between the microbiome and human health. The diverse applications across research, diagnostics, and therapeutics suggest a broad and expanding market with significant future potential, particularly in personalized medicine and precision healthcare.

The Global Metagenomic Sequencing Market Size Was Worth $1.99 Billion in 2023 and Is Expected To Reach $6.21 Billion by 2032, At a CAGR of 13.50%.

This repository contains raw and intermediate data files as well as analysis code from the manuscript "Evaluating the Analytical Performance of Direct-to-Consumer Gut Microbiome Testing Services". In this analysis a pilot version of the homogenized whole human stool reference material was submitted as a sample to commercial direct to consumer microbiome testing companies. In addition, NIST conducted in house characterization by 16S amplicon sequencing and whole metagenomic sequencing (WMS) on the same sample. Raw sequencing data from the sequencing providers was not obtained for this study; however sequencing files (fastq) both 16S amplicon sequencing analysis and whole metagenomic sequencing (WMS) conducted at NIST are included. In addition, the fastq files from other donors that contributed to the pilot material and included in this analysis to represent biological diversity are also included in this record.

Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also be a function of PCR product exhaustion during sequencing. To further examine theses biases, data is provided from 16S rRNA rumen community analyses. Specifically, data from the relative phylum-level abundances for the ruminal bacterial community are provided to determine between-sample variability. Direct sequencing of metagenomic DNA was conducted to circumvent primer-associated biases in 16S rRNA reads and rarefaction curves were generated to demonstrate adequate coverage of each amplicon. PCR products were also subjected to reduced amplification and pooling to reduce the likelihood of PCR product exhaustion during sequencing on the Pacific Biosciences platform. The taxonomic profiles for the relative phylum-level and genus-level abundance of rumen microbiota as a function of PCR pooling for sequencing on the Pacific Biosciences RSII platform were provided. Data is within this article and raw ruminal MiSeq sequence data is available from the NCBI Sequence Read Archive (SRA Accession SRP047292). Additional descriptive information is associated with NCBI BioProject PRJNA261425. http://www.ncbi.nlm.nih.gov/bioproject/PRJNA261425/ Resources in this dataset:Resource Title: NCBI Sequence Read Archive (SRA Accession SRP047292). File Name: Web Page, url: https://www.ncbi.nlm.nih.gov/sra/SRX704260 1 ILLUMINA (Illumina MiSeq) run: 978,195 spots, 532.9M bases, 311.6Mb downloads.

The global microbiome sequencing services market is experiencing robust growth, with a market size of $1.71 billion in 2025 and a projected Compound Annual Growth Rate (CAGR) of 6.70% from 2025 to 2033. This expansion is driven by several key factors. Advancements in sequencing technologies, such as Sequencing by Ligation (SBL), Sequencing by Synthesis (SBS), Shotgun Sequencing, and Targeted Gene Sequencing, are reducing costs and increasing throughput, making microbiome analysis more accessible for research and clinical applications. The rising prevalence of chronic diseases like gastrointestinal disorders, infectious diseases, CNS diseases, and cancer, coupled with a growing understanding of the microbiome's role in these conditions, fuels demand for these services. Furthermore, increasing investments in research and development, coupled with the growing adoption of personalized medicine approaches which leverage microbiome data for diagnosis and treatment, are significant drivers. Key market trends include the emergence of cloud-based microbiome analysis platforms, the development of novel bioinformatics tools for data interpretation, and the increasing integration of microbiome sequencing into clinical workflows. However, challenges remain, including the high cost of advanced sequencing technologies, the complexity of data analysis, and the lack of standardized protocols for microbiome research, which act as market restraints. The market is segmented by technology and application, with Sequencing by Synthesis (SBS) currently dominating the technology segment, and Gastrointestinal Diseases and Oncology leading the application segment. Geographically, North America and Europe currently hold significant market shares, driven by robust healthcare infrastructure and substantial research funding. The competitive landscape is characterized by a mix of established players and emerging companies, including ZIFO, Baseclear BV, Metabiomics, Zymo Research, Microbiome Insights Inc, CosmosID, Shanghai Realbio Technology (RBT) Co Ltd, Rancho Biosciences, Merieux Nutrisciences Corporations (Biofortis), Clinical Microbiomics AS, MR DNA, and Locus Biosciences (EPIBIOME), among others. These companies are actively engaged in developing innovative technologies, expanding their service offerings, and forging strategic partnerships to gain a competitive edge. The market is expected to witness increased consolidation and strategic acquisitions in the coming years. Future growth will be significantly influenced by the development of more accurate and cost-effective sequencing technologies, the expansion of clinical applications, the establishment of standardized data analysis pipelines, and the growing adoption of microbiome-based therapeutics. The Asia Pacific region presents a significant growth opportunity due to rising healthcare expenditure, increasing awareness of microbiome research, and a growing prevalence of chronic diseases. Continued research into the complex interplay between the microbiome and human health will undoubtedly shape the future trajectory of this rapidly expanding market, driving further innovation and market penetration across various geographical regions and application areas. This report provides a detailed analysis of the Microbiome Sequencing Services market, projected to reach multi-billion dollar valuations in the coming years. It examines market concentration, key trends, dominant segments, leading players, and significant recent developments. Recent developments include: November 2023: QIAGEN NV launched the Microbiome WGS (whole-genome sequencing) SeqSets which is a comprehensive Sample to Insight workflow designed to provide an easy-to-use solution that maximizes efficiency and reproducibility in microbiome research., June 2023: Zymo Research launched its full-length 16S sequencing service offering researchers high-quality, full-length 16S rRNA gene sequencing for microbiome analysis.. Key drivers for this market are: Huge Investment in Microbiome Research, Rise in Demand for NGS Services; Surge in Genomic Research and Widening Application Area of Microbiome Sequencing. Potential restraints include: Ethical and Legal Issues Related to Genome Sequencing, Lack of Skilled Technicians for NGS Data Analysis. Notable trends are: The Oncology Segment is Expected to Hold a Significant Market Share Over the Forecast Period.

Archival DNA samples collected and analysed for a range of research and applied questions have accumulated in the laboratories of universities, government agencies, and commercial service providers for decades. These DNA archives represent a valuable, yet largely untapped repository of genomic information. With lowering costs of, and increasing access to, high-throughput sequencing, we predict an increase in retrospective research to explore the wealth of information that resides in these archival samples. However, for this to occur, we need confidence in the integrity of the DNA samples, often stored under sub-optimal conditions and their fitness of purpose for downstream genomic analysis. Here, we borrow from a well-established concept in ancient DNA to evaluate sample integrity, defined as loss of information content in recovered amplicons, of frozen DNA samples and based on the ratio of ⠺-diversity of short and long-read 16S rRNA gene sequences. The 16S rRNA variable region of eight..., Data analysis The Pacific Biosciences Nextflow pipeline (https://github.com/PacificBiosciences/pb-16S-nf) was followed for initial data processing. Raw reads were processed, including demultiplexing by “q2-demux†in QIIME2, and quality control was assessed with q2-cutadapt. Quantitative Insights Into Microbial Ecology 2 (QIIME2 v. 2018.11) software was used to analyse the trimmed reorientated sequences (Bolyen et al., 2019). The DADA2 denoising option (Callahan et al., 2016) was selected to pick up the representative reads for generating an amplicon sequence variants (ASVs) table. ASVs generated from DADA2 were classified using the Naive Bayes classifier and SILVA reference database version 138.1 (Quast et al., 2013). For analysis between the platforms the feature table of each platform was merged, as were the representative sequences post-DADA2 denoising with QIIME2 before building the phylogenetic tree and assigning taxonomy. Taxonomic diversity analysis All analysis was conducted wit..., , # A novel method to assess the integrity of frozen archival DNA samples: Alpha-diversity ratios of short and long-read 16S rRNA gene sequences

https://doi.org/10.5061/dryad.v9s4mw73t

We utilized DNA extracted from various agricultural soils that were stored at -20°C in a gene bank freezer room over 20 years by the South Australian Research and Development Institute (SARDI). This DNA was collected through the PREDICTA® B DNA-based soil disease testing service for broadacre farming (PREDICTA® B). We selected 87 soil DNA extracts from three Australian states (regions), spanning 10 distinct time bins between 2001 and 2020. Our primary concern was the potential DNA degradation in the oldest samples. Therefore, we included samples from the first four years (2001-2004) and selected samples more sporadically from subsequent years (2005 onwards). Alpha-diversity ratios, using Shannon's diversity index, were calculated to determine if there was a d...

According to Cognitive Market Research, the global Microbiome Sequencing Services market size will be USD 1529.8 million in 2025. It will expand at a compound annual growth rate (CAGR) of 11.50% from 2025 to 2033.

North America held the major market share for more than 40% of the global revenue with a market size of USD 566.03 million in 2025 and will grow at a compound annual growth rate (CAGR) of 9.3% from 2025 to 2033.
Europe accounted for a market share of over 30% of the global revenue with a market size of USD 443.64 million.
APAC held a market share of around 23% of the global revenue with a market size of USD 367.15 million in 2025 and will grow at a compound annual growth rate (CAGR) of 13.5% from 2025 to 2033.
South America has a market share of more than 5% of the global revenue with a market size of USD 58.13 million in 2025 and will grow at a compound annual growth rate (CAGR) of 10.5% from 2025 to 2033.
The Middle East had a market share of around 2% of the global revenue and was estimated at a market size of USD 61.19 million in 2025 and will grow at a compound annual growth rate (CAGR) of 10.8% from 2025 to 2033.
Africa had a market share of around 1% of the global revenue and was estimated at a market size of USD 33.66 million in 2025 and will grow at a compound annual growth rate (CAGR) of 11.2% from 2025 to 2033.
Sequencing by Synthesis category is the fastest growing segment of the Microbiome Sequencing Services industry

Market Dynamics of Microbiome Sequencing Services Market

Key Drivers for Microbiome Sequencing Services Market

Rising Prevalence of Chronic Diseases and Lifestyle Disorders to Boost Market Growth

The increasing incidence of chronic conditions such as obesity, diabetes, gastrointestinal disorders, and autoimmune diseases is a major driver of the microbiome sequencing services market. Research increasingly shows that gut microbiota plays a significant role in immune system regulation, metabolism, and inflammation pathways—critical factors in the development and progression of chronic illnesses. This has heightened the interest of healthcare providers and researchers in microbiome analysis to understand disease mechanisms, identify microbial biomarkers, and develop microbiome-targeted therapies. Additionally, lifestyle changes, poor dietary habits, and environmental exposures further disrupt the gut microbial balance, leading to demand for advanced diagnostic services. Microbiome sequencing enables high-resolution analysis of microbial diversity, composition, and function, helping to tailor personalized treatment plans. For instance, OraSure Technologies, under its Diversigen arm, introduced a service for gut microbiota sample metatranscriptomic sequencing and analysis, advancing capabilities in understanding microbiome dynamics for research and clinical applications.

https://orasure.com/

Advancements in Next-Generation Sequencing (NGS) Technologies To Boost Market Growth

Technological innovations, particularly in next-generation sequencing (NGS), are significantly accelerating the growth of microbiome sequencing services. Modern NGS platforms offer rapid, high-throughput, and cost-effective methods to analyze complex microbial communities with unmatched accuracy and depth. These advancements allow researchers to sequence millions of DNA fragments simultaneously, leading to comprehensive profiling of microbial genomes and their functional genes. Furthermore, the integration of bioinformatics and cloud-based data analysis tools enhances the interpretation of massive datasets generated through sequencing, enabling more meaningful insights into microbiome roles in health and disease.

Restraint Factor for the Microbiome Sequencing Services Market

High Cost of Sequencing and Data Analysis Will Limit Market Growth

The major restraining factor for the microbiome sequencing services market is the high cost associated with sequencing procedures and subsequent data analysis. Although the cost of sequencing technologies like 16S rRNA and whole-genome shotgun sequencing has decreased over time, it still remains substantial, particularly for large-scale or longitudinal studies. Additionally, the infrastructure required for sample processing, high-throughput sequencing platforms, and advanced bioinformatics tools significantly increases the overall project cost. Many small- to mid-sized research labs, clinical settings, or biotech st...

Soil Microbiome Sequencing Services Market Outlook

According to our latest research, the soil microbiome sequencing services market size reached USD 1.18 billion in 2024, reflecting robust expansion driven by heightened interest in sustainable agriculture and environmental monitoring. The market is projected to grow at a CAGR of 13.7% from 2025 to 2033, with the forecasted market size expected to reach USD 3.74 billion by 2033. This remarkable growth is primarily attributed to the increasing adoption of advanced sequencing technologies and the rising demand for precise soil health assessment across diverse sectors.

One of the primary growth factors for the soil microbiome sequencing services market is the surge in global emphasis on sustainable agricultural practices. As food security and soil fertility become critical concerns, stakeholders across the agricultural value chain are increasingly leveraging microbiome sequencing to understand and optimize the complex interactions between soil microorganisms and crop health. This has led to a significant uptick in demand for sequencing services that can provide actionable insights into nutrient cycling, disease resistance, and yield enhancement. The growing awareness among farmers and agronomists regarding the benefits of microbiome-based soil management is further amplifying market growth, with governments and international organizations supporting research initiatives aimed at improving soil health and productivity.

Another pivotal driver is the technological advancement in sequencing methodologies, which has made soil microbiome analysis more accessible, accurate, and cost-effective. Innovations such as high-throughput 16S rRNA sequencing, shotgun metagenomics, and whole genome sequencing are enabling the comprehensive profiling of soil microbial communities at unprecedented depth and resolution. These advancements are not only reducing the turnaround time for sequencing projects but also expanding the scope of applications beyond agriculture to include environmental monitoring, industrial bioremediation, and ecosystem restoration. The integration of bioinformatics and AI-driven data analysis tools is further streamlining the interpretation of complex sequencing data, thereby enhancing the utility and value proposition of soil microbiome sequencing services for end-users.

The expansion of collaborative research and public-private partnerships is also fueling the growth of the soil microbiome sequencing services market. Academic institutions, research organizations, and commercial enterprises are increasingly pooling resources to undertake large-scale soil microbiome studies aimed at addressing global challenges such as climate change, land degradation, and biodiversity loss. These collaborations are resulting in the development of standardized protocols, shared databases, and open-access platforms that are accelerating knowledge dissemination and technology adoption. Moreover, increased funding from governmental and non-governmental sources for soil health research is providing a strong impetus to service providers, enabling them to expand their service portfolios and geographic reach.

From a regional perspective, North America currently dominates the soil microbiome sequencing services market, supported by a well-established agricultural sector, advanced research infrastructure, and strong demand for precision farming solutions. Europe follows closely, driven by stringent environmental regulations and a growing focus on sustainable land management. The Asia Pacific region is witnessing the fastest growth, underpinned by large-scale agricultural activities, rising investments in research and development, and increasing awareness about soil health among policymakers and industry stakeholders. Latin America and the Middle East & Africa are also emerging as promising markets, propelled by efforts to enhance agricultural productivity and address environmental concerns.

Sequencing Technology Analysis

The sequencing technology segment forms the backbone of the soil microbiome sequencing services market, encompassing a range of advanced methodologies that enable the detailed analysis of soil microbial communities. 16S rRNA sequencing remains a widely adopted technique due to its cost-effectiveness and ability to provide comprehensive taxonomic profiling of bacterial populations. This method is particularly favored in academic and research settings where large-

Der globale Markt für metagenomische Sequenzierung hatte im Jahr 2023 einen Wert von 1.99 Milliarden US-Dollar und dürfte bis 2032 einen Wert von 6.21 Milliarden US-Dollar erreichen, bei einer durchschnittlichen jährlichen Wachstumsrate von 13.50 %.

La taille du marché mondial du séquençage métagénomique valait 1.99 milliard de dollars en 2023 et devrait atteindre 6.21 milliards de dollars d'ici 2032, à un TCAC de 13.50 %.

Certain occupational and geographical exposures have been associated with an increased risk of lung disease. As a baseline for future studies, we sought to characterize the upper respiratory microbiomes of healthy military personnel in a garrison environment. Nasal, oropharyngeal, and nasopharyngeal swabs were collected from 50 healthy active duty volunteers eight times over the course of one year (1107 swabs, completion rate = 92.25%) and subjected to pyrosequencing of the V1–V3 region of 16S rDNA. Respiratory bacterial taxa were characterized at the genus level, using QIIME 1.8 and the Ribosomal Database Project classifier. High levels of Staphylococcus, Corynebacterium, and Propionibacterium were observed among both nasal and nasopharyngeal microbiota, comprising more than 75% of all operational taxonomical units (OTUs). In contrast, Streptococcus was the sole dominant bacterial genus (approximately 50% of all OTUs) in the oropharynx. The average bacterial diversity was greater in the oropharynx than in the nasal or nasopharyngeal region at all time points. Diversity analysis indicated a significant overlap between nasal and nasopharyngeal samples, whereas oropharyngeal samples formed a cluster distinct from these two regions. The study produced a large set of pyrosequencing data on the V1–V3 region of bacterial 16S rDNA for the respiratory microbiomes of healthy active duty Service Members. Pre-processing of sequencing reads showed good data quality. The derived microbiome profiles were consistent both internally and with previous reports, suggesting their utility for further analyses and association studies based on sequence and demographic data.

These data consist of raw 16S rRNA gene sequences for the bacterial communities in three upland Welsh river sites under different treatments. A mapping file with metadata for each sample is provided and a operational taxonomic unit (OTU) table. These sites were situated in three streams from the Llyn Brianne Stream Observatory, Powys, Wales, UK (52°08' N, 3°45' W). The catchments cover approximately 300 square kilometres of upland Wales in the upper Afon Tywi. These first to third order experimental streams rise in either rough, sheep-grazed moorland (named as L6 and L7) or plantations of Sitka spruce Picea sitchensis with lodgepole pine Pinus contorta (named as L3). Some reductions of forest cover have occurred in L3 with normal logging operations. A 24-hour experiment was conducted at the Diversity in Upland Rivers for Ecosystem Service Sustainability (DURESS) cascading flumes at these streams during September 2014. Each flume consisted of 3 channels, each assigned a different treatment: control, sugar addition and peat addition. Sugar (sucrose) and peat were added to channels to represent a simple and complex form of dissolved organic carbon (DOC) respectively. Five biofilm samples were collected from random locations in each experimental channel. Samples were taken at 0.5, 3, 15 and 24 hours after the start of the experiment. Epilithon were taken from unglazed ceramic tiles that had been colonised by epilithon in the river. After amplification, the 16S rRNA fragments were sequenced on the Illumina MiSeq next generation sequencing platform. The main goal of this survey was to characterise bacterial diversity, the chemical and biological consequences of elevated DOC inputs, and to investigate the role of bacterial organisms in controlling organic carbon flux. Prof Andy Weightman and Dr Isabelle Durance were responsible for organising the experiments. Sampling was carried out by Dr. Isa-Rita Russo and a team of Post Doctoral Research Assistants (PDRA's)/students. The work was carried out under the Diversity in Upland Rivers for Ecosystem Service Sustainability (DURESS) project (Grant reference NERC NE/J014818/1). DURESS was a project funded by the Natural Environment Research Council (NERC) Biodiversity and Ecosystem Service Sustainability (BESS) programme. Full details about this dataset can be found at https://doi.org/10.5285/df829b9f-c4c5-4e53-9217-c9c1e5bd078d

A publicly-accessible website to measure and visualize similarities and differences between molecular profiles of complex microbial communities. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally.

ABSTRACT

The complexity of brain circuits is sculpted both by innate genetic programs and environmental stimuli. Since the 1960s scientists have noticed that raising rodents in an enriched environment (EE) is able to improve all aspects of brain plasticity, from learning and memory to visual plasticity in adult and developing animals. Importantly, EE has also been shown to have beneficial effects on a variety of preclinical models of central nervous system diseases: Alzheimer’s and Parkinson’s disease, Rett syndrome, epilepsy etc, prompting intervention protocols in humans. However, the “enrichment derived key signals” through which this special environment performs its broad positive effects on brain health have not been completely elucidated yet. Here, we focused on signals coming from the body periphery and in particular on the gut microbiota. We found that the intestinal microbiota composition of EE mice is significantly different from the one of standard raised (ST) animals. Treatment of EE mice with an antibiotic cocktail completely prevented the EE-driven enhancement of OD plasticity. Strikingly, the fecal microbiota transplant from EE donors to adult ST mice was able to re-activate OD plasticity in the ST recipients. Thus, taken together our data suggest that experience-dependent changes in gut microbiota regulate brain plasticity.

METHODS

In the first dataset (Dataset1, files called zr2423) we report the raw data (.fastq) obtained from the sequencing of the fecal samples from C57BL/6J mice raised in EE or in ST from birth and collected at different time points during their lives.

To analyze the composition of the microbiota of ST and EE mice at different ages, fresh faeces were collected longitudinally in the same subject at postnatal day (P)20 (n=6), P25 (n=6) and P90 (n=6).

In the second dataset (Dataset2, files called zr2747) we report the raw data (.fastq) obtained from the sequencing of the fecal samples from C57BL/6J: adult donor mice living in EE (EE, n=8), adult recipient mice living in ST condition before the fecal transplantation (preFT, n=8) and 4 weeks after the fecal transplantation (postFT, n=8).

For further details about the sample names see the “Explanation Table”.

Bacterial DNA was extracted using a specific kit (QIAamp Powerfecal DNA kit, Qiagen) following the manufacturer's protocol. The 16S rRNA sequencing and analysis was performed by a service offered by Zymo Research (Irvine, CA, USA).

Targeted Library Preparation: The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research). The primer sets used were Quick-16S™ Primer Set V3-V4 (Zymo Research). The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™, then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA).

Sequencing: The final library was sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cycles). The sequencing was performed with >10% PhiX spike-in.

This study investigated soil and groundwater contamination at an in-service oil transportation station in the middle-lower Yellow River Basin, China. Spatial analysis combined with 16S rRNA and ITS sequencing revealed localized heavy metal (Cu, Ni, Cd, Pb) and petroleum hydrocarbon (PHs: 15.0 mg/kg) contamination in the oily sewage treatment area, with vertical migration constrained by silty sand layers. Volatile organic compounds (VOCs) primarily originated from oil tank emissions. Groundwater exhibited hydraulic gradient-driven downstream migration of PHs (0.03–0.04 mg/L) and arsenic (1.1–1.5 μg/L). Indigenous microbial communities exhibited redox-stratified functional differentiation: unclassified Comamonadaceae (Proteobacteria) dominated aerobic zones (monitoring well D5), utilizing nitrate for PHs degradation, while Desulfosporosinus (Firmicutes) mediated sulfate-coupled anaerobic alkane degradation and metal immobilization in anoxic zones (D6). Fungal communities featured Trametes (Basidiomycota), facilitating ligninolytic PAH breakdown via peroxidase secretion. Functional prediction (FAPROTAX/FUNGuild) confirmed a synergistic “fungal preprocessing-bacterial mineralization” mechanism. Microbial metabolic plasticity (e.g., nitrogen respiration, photoautotrophy) enabled adaptation to redox fluctuations. Given the site’s medium-low risk profile, we proposed a tiered management framework: (1) in situ bioremediation that prioritizes indigenous microbes, (2) hierarchical risk zoning, and (3) dynamic monitoring networks. These strategies align with China’s Green Low-Carbon Remediation principles through low-energy microbial technologies. The findings provide a mechanistic basis for balancing industrial operations and ecological health in the Yellow River Basin.

See the referenced paper for additional details.

Sampling. Sampling was conducted on board the RSV Aurora Australis during cruise V3 from 20 January to 7 February 2012. This cruise occupied a latitudinal transect from waters north of Cape Poinsett, Antarctica (65_ S) to south of Cape Leeuwin, Australia (37_ S) within a longitudinal range of 113-115_ E. Sampling was performed as described in ref. 29, with sites and depths selected to provide coverage of all major SO water masses. At each surface station, E250-560 l of seawater was pumped from E1.5 to 2.5m depth. At some surface stations, an additional sample was taken from the Deep Chlorophyll Maximum (DCM), as determined by chlorophyll fluorescence measurements taken from a conductivity, temperature and depth probe (CTD) cast at each sampling station. Samples of mesopelagic and deeper waters (E120-240 l) were also collected at some stations using Niskin bottles attached to the CTD. Sampling depths were selected based on temperature, salinity and dissolved oxygen profiles to capture water from the targeted water masses. Profiles were generated on the CTD descent, and samples were collected on the ascent at the selected depths. Deep water masses were identified by the following criteria: CDW 1/4 oxygen minimum (Upper Circumpolar Deep) or salinity maximum (Lower Circumpolar Deep); AABW 1/4 deep potential temperature minimum; AAIW 1/4 salinity minimum 18. The major fronts of the SO, which coincide with strong horizontal gradients in temperature and salinity 19,30, separate regions with similar surface water properties. The AZ lies south of the Polar Front (which was at 51_ S during sampling), whereas the PFZ lies between the Polar Front and the Subantarctic Front. In total, 25 samples from the AZ, PFZ, SAMW, AAIW, CDW and AABW were collected for this study (Fig. 1, Supplementary Data 1). Seawater samples were prefiltered through a 20-mm plankton net, biomass captured on sequential 3.0-, 0.8- and 0.1-mm 293-mm polyethersulphone membrane filters and filters immediately stored at _80 _C31,32.

DNA extraction and sequencing. DNA was extracted with a modified version of the phenol-chloroform method 31. Tag pyrosequencing was performed by Research and Testing Laboratory (Lubbock, USA) on a GS FLXb platform (Roche, Branford, USA) using a modification of the standard 926F/1392R primers targeting the V6-V8 hypervariable regions of bacterial and archaeal 16S rRNA genes (926wF: 50-AAA-CTY-AAA-KGA-ATT-GRC-GG-30 , 1,392 R: 50-ACG-GGCGGT-GTG-TRC-30). Denoising, chimera removal and trimming of poor quality read ends were performed by the sequencing facility.