Jinjun Kan

• Ph. D
• Research Associate at Stroud Water Research Center, Avondale, United States

The seasonal controls of hydrology, temperature, hypoxia, and biogeochemical conditions for groundwater ammonium–N (NH4⁺) concentrations are not well understood. Here we investigated these controls for riparian groundwaters located upstream of two milldams over a period of 4 years. Groundwater chemistry was sampled monthly while groundwater elevati...

Light plays a crucial role in microbiomes, maintaining the amount and transfer of primary productivity and directing ecosystem functioning. Coastal microbiomes are frequently exposed to light-limited conditions, but how their community organization is affected remains unclear. This study aimed to investigate the assembly, association and functional...

Stream and floodplain restoration is a popular billion-dollar industry in the United States, with many restorations being conducted to satisfy water pollution regulations and nutrient reduction goals. The long-term efficacy of these restorations is, however, not well studied, and key soil metrics that can be used for performance assessments have no...

Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decrease...

Water column removal in streams is a nitrogen (N) cycling pathway that has been historically overlooked. Studies filling this knowledge gap have focused on the role of water column N removal in mid‐to‐large‐order rivers with consistently high suspended sediment concentrations. However, smaller streams may provide comparable suspended sediment conce...

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) compete in reducing sediment conditions where DNF permanently removes nitrogen (N), while DNRA retains N with the conversion of nitrate (NO3–) to ammonium (NH4+). Thus, an increase in the level of DNRA can undermine permanent N removal. We investigated the relative magnitu...

SAR202 bacteria in the Chloroflexota phylum are abundant and widely distributed in the ocean. Their genome coding capacities indicate their potential roles in degrading complex and recalcitrant organic compounds in the ocean. However, our understanding of their genomic diversity, vertical distribution, and depth-related metabolisms is still limited...

Interstitial water or pore water occupies the space between soil particles and provides “hotspots” and “fluvial networks” for microbial activities in floodplain soil. However, to date, we know very little about the microorganisms living in pore water and how they respond to environmental changes. This study aimed to understand microbial distributio...

Phytoplankton are important drivers of aquatic ecosystem function and environmental health. Their community compositions and distributions are directly impacted by environmental processes and human activities, including in the largest estuary in North America, the Chesapeake Bay. It is crucial to uncover how planktonic eukaryotes play fundamental r...

Groundwater nitrate-N isotopes (δ 15 N-NO 3) have been used to infer the effects of natural and anthropogenic change on N cycle processes in the environment. Here we report unexpected changes in groundwater δ 15 N-NO 3 for riparian zones affected by relict milldams and road salt salinization. Contrary to natural, undammed conditions, groundwater δ...

The Mariana Trench, a stable marine ecosystem minimally impacted by human activities, has the greatest vertical depth in the ocean. Depth gradients profoundly influence the physical, chemical, and biotic conditions in the deep oceans. Therefore, elucidating the depth-related effects on microbiome assembly and interaction is integral to understandin...

Stream, floodplain, and wetland restorations enhance water quality and ecological function; however, soil health is prioritized infrequently in restoration planning and monitoring. Buried, historic, hydric soils—common across U.S. mid-Atlantic valley bottoms beneath legacy sediments—are not included in most floodplain restoration designs, though th...

Nitrogen (N) pollution in riverine ecosystems has substantial environmental, economic, and policy consequences. Various riverine N removal processes include permanent dissimilatory sinks such as denitrification (Uden) and temporary assimilatory sink such as microbial N uptake (Uassim). Both processes have been extensively evaluated in benthic sedim...

Introduction Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies alterin...

The diversity and primary productivity in the Arctic ecosystem are rapidly changing due to global warming. Microorganisms play a vital role in biogeochemical cycling. However, the diversity of planktonic microorganism communities in the Laptev Sea, one of the most important marginal seas of the Western Arctic Ocean, have not been studied sufficient...

The compounding effects of anthropogenic legacies for environmental pollution are significant, but not well understood. Here, we show that centennial‐scale legacies of milldams and decadal‐scale legacies of road salt salinization interact in unexpected ways to produce hot spots of nitrogen (N) in riparian zones. Riparian groundwater and stream wate...

As and Hg were examined in the Yellowstone Lake food chain, focusing on two lake locations separated by ~20 km and that differed in lake floor hydrothermal vent activity. Sampling spanned from femtoplankton to the main fish species, Yellowstone Cutthroat Trout and the apex predator Lake Trout. Hg bioaccumulated in muscle and liver of both trout spe...

Despite significant advances in our understanding of nitrogen (N) removal pathways along river networks, the role of water column processes remains largely understudied. This knowledge gap not only limits our capacity to determine N transport and retention in mid-to-large rivers but also hampers our understanding of N removal processes in smaller s...

Biofilm communities play a major role in explaining the temporal variation of biogeochemical conditions in freshwater ecosystems, and yet we know little about how these complex microbial communities change over time (aka succession), and from different initial conditions, in comparison to other stream communities. This has resulted in limited knowl...

This study contributes to our evolving understanding of how coupled biogeochemical dynamics of Fe and Mn along the redox gradients affect C cycling and sequestration at Critical Zones. A 12-month monitoring of the in-situ soil pore-water biogeochemistry and redox gradients across the floodplain at the White Clay Creek Watershed in the Christina Riv...

Background Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurr and how the inter-taxa networks respond to the strong environmental gradien...

Large storms can erode, transport, and deposit substantial amounts of particulate nitrogen (PN) in the fluvial network. The fate of this input and its consequence for water quality is poorly understood. This study investigated the transformation and leaching of PN using a 56-day incubation experiment with five PN sources: forest floor humus, upland...

The microbial carbon pump (MCP) provides a mechanistic illustration of transformation of recalcitrant dissolved organic matter (DOM) in the ocean. Here, we explored and demonstrated the key roles of algae-associated microorganisms (mainly heterotrophic bacteria) in the production and transformation of carboxyl-rich alicyclic molecule (CRAM)-like DO...

Background: Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurrence with each other and how the inter-taxa networks respond to the strong...

Dam removals are on the increase across the US with Pennsylvania currently leading the nation. While most dam removals are driven by aquatic habitat and public safety considerations, we know little about how dam removals impact water quality and riparian zone processes. Dam removals decrease the stream base level, which results in dewatering of the...

Marine bacterial community plays a vital role in the formation of the hypoxia zone in coastal oceans. Yet, their dynamics in the seasonal hypoxia zone of the Bohai Sea (BHS) are barely studied. Here, the 16S rRNA gene-based high-throughput sequencing was used to explore the dynamics of their diversity, structure, and function as well as driving fac...

The soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of p...

Skeletonema dohrnii is a common red tide microalgae occurring in the coastal waters and throughout the world. The associated heterotrophic or autotrophic bacteria play vital roles in regulating algal growth, production, and physiology. In this study, we investigated the detailed bacterial community structure associated with the growth of S. dohrnii...

Milldams and their legacies have significantly influenced fluvial processes and geomorphology. However, less is known about their effects on riparian zone hydrology, biogeochemistry, and water quality. Here, we discuss the potential effects of existing and breached milldams on riparian nitrogen (N) processing through multiple competing hypotheses a...

Marine chromophytic phytoplankton are a diverse group of algae and contribute significantly to the total oceanic primary production. However, the spatial distribution of chromophytic phytoplankton is understudied in the West Pacific Ocean (WPO). In this study, we have investigated the community structure and spatial distribution of chromophytic phy...

Background: Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa interact with each other (e.g., mutualistic and competitive interactions) and how t...

In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United S...

Chesapeake Bay is a large, dynamic, and productive temperate estuary, which plays an important role in transporting terrestrial materials into the Atlantic Ocean. The bacterioplankton communities experience strong environmental changes both seasonally and along the central axis of the Bay. The goal of this study was to explore the spatiotemporal an...

While stream restorations are increasingly being adopted to mitigate sediment and nutrient inputs and to meet water quality regulatory targets, less information is available on the drivers behind the design, implementation, effectiveness, and cost of restorations. We address these issues for a $4.2 million stream restoration for legacy sediments im...

While streambank legacy sediment has been increasingly recognized as an important contributor of fine sediment to watersheds, little is known about its contributions to suspended sediment‐bound nutrients. This uncertainty is exacerbated by the ubiquitous presence of legacy sediments in valley‐bottoms of the Mid‐Atlantic region of the United States....

Streambank legacy sediments can contribute substantial amounts of sediments to Mid-Atlantic waterways. However, there is uncertainty about the sediment-bound P inputs and the fate of legacy sediment P in surface waters. We compared legacy sediment P concentrations against other streambank sediments and upland soils and evaluated a variety of P indi...

Streambank legacy sediments may be important sources of sediment and nutrients from Mid-Atlantic watersheds. However, little is known about the nutrient processing roles of microorganisms that inhabit legacy sediments, let alone their composition, diversity, and distributions. In this study, we sampled 15 streambanks at multiple depths throughout f...

Concentrations of nutrients and heavy metals in streambank legacy sediments are needed to estimate watershed exports and to evaluate against upland inputs. Concentrations of nutrients and heavy metals were determined for legacy sediments in 15 streambanks across northeastern Maryland, southeastern Pennsylvania, and northern Delaware. Samples were c...

Viruses have important impacts on aquatic microbial ecology and have been studied at length in the global ocean. However, the roles of bacteriophages in lotic ecosystems, particularly in benthic biofilms, have been largely under-studied. The main goals of this work were to determine whether viruses are consistent members of natural benthic biofilm...

The diazotrophic communities play an important role in sustaining primary productivity through adding new nitrogen to oligotrophic marine ecosystems. Yet, their composition in the oligotrophic Indian Ocean is poorly understood. Here, we report the first observation of phylogenetic diversity and distribution of diazotrophs in the Eastern Indian Ocea...

Phytoplankton are the basis of primary production and play important roles in regulating energy export in marine ecosystems. Compared to other regions, chromophytic phytoplankton are considerably understudied in the Bay of Bengal (BOB). Here, we investigated community structure and spatial distribution of chromophytic phytoplankton in the BOB by us...

The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sedimen...

High-biomass red tides occur frequently in some semi-enclosed bays of Hong Kong where ambient nutrients are not high enough to support such a high phytoplankton biomass. These high-biomass red tides release massive inorganic nutrients into local waters during their collapse. We hypothesized that the massive inorganic nutrients released from the col...

Large rainstorms deliver significant amounts of upland materials to headwater streams, thereby introducing the particle-associated microorganisms from complex soil environments into stream networks. "Seeding and mixing" from terrestrial sources may generate "new" in-stream microbial consortia and facilitate nutrient transformations and export to re...

Large storm events possess significant erosive energy capable of mobilizing large amounts of sediment and particulate organic matter (POM) into fluvial systems. This study investigated how stream POM composition varied as a function of the watershed POM source, particle size, storm event magnitude, and seasonal timing. POM composition was character...

Climate models predict increased frequency and intensity of storm events, but it is unclear how extreme precipitation events influence the dynamics of soil fluxes for multiple greenhouse gases (GHGs). Intact soil mesocosms (0–10 cm depth) from a temperate forested watershed in the piedmont region of Maryland [two upland forest soils, and two hydric...

Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) wer...

Carbon-mineral association between iron oxides and dissolved organic carbon (DOC) occurs ubiquitously in natural environments, and is thus an important control on the transport and sequestration of organic carbon. However, the stability of C-mineral association under reducing conditions and its implication on carbon turnover and cycling is unclear....

Besides being critical components of marine food web, microorganisms play vital roles in biogeochemical cycling of nutrients and elements in the ocean. Currently little is known about microbial population structure and their distributions in the eastern Indian Ocean. In this study, we applied molecular approaches including polymerase chain reaction...

Soil microbial community (SMC) structure affects several ecosystem services (soil-carbon mineralization and stabilization), yet responds to edaphic conditions. Stemflow, water that drains over the exterior surface of trees, concentrates precipitation to soils near the trunk, thereby altering edaphic conditions.While recognizing that a suite of fact...

Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Qu...

Detailed identification of bacterial sequences and their classification at Phylum, Class, Order, Family, and Genus levels.

Detailed identification of archaeal sequences and their classification at Phylum, Class, Order, Family, and Genus levels.

Yellowstone Lake (Yellowstone National Park, WY, USA) is a large high-altitude (2200 m), fresh-water lake, which straddles an extensive caldera and is the center of significant geothermal activity. The primary goal of this interdisciplinary study was to evaluate the microbial populations inhabiting thermal vent communities in Yellowstone Lake using...

Nannochloropsis is an ubiquitous genus, found in diverse aquatic environments including open ocean as well as fresh and brackish water. Recently, large-scale blooms occurred frequently along eutrophic coastal zone from the Bohai Sea to the northern Yellow Sea in China. The cell density reached 10(9) to 10(10)cells per liter during a bloom near Qinh...

Diversity and structure of the soil microbial community (SMC) significantly affects soil ecosystem services including, nutrient cycling, C-mineralization, and stabilization/formation of soil structure. SMC also responds to changes in soil moisture and chemistry. Stemflow, the concentration of precipitation to soils at the trunk base, is well known...

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to understanding of patterns in nutrient cycling and related ecological services. Since forest canopy structure alters the spatiotemporal patterning of precipitation water and solute supplies to soils (via the “throughfall” mechanism), is it possible chang...

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to our understanding of patterns in biogeochemical cycling and related ecological services (e.g., plant community structure, water quality, response to environmental change). Since forest canopy structure alters the spatiotemporal patterning of precipitati...

Seasonal shifts of dissolved inorganic nitrogen (DIN) and the dynamics of microbial communities for nitrogen transformation were investigated in the water column of Chesapeake Bay. The relative abundance of nitrogen over phosphorus (N*) showed a strong seasonal and spatial pattern: gradually decreased from upstream to downstream; high in winter and...

Cathode reaction is one of the most serious limiting factors in a microbial fuel cell (MFC). The critical dissolved oxygen (DO) concentration of platinum loaded graphite electrode was reported as 2.2 mg/1 that is about 10-fold higher than an aerobic bacteria. A series of MFCs were run with cathode compartment inoculated with activated sludge (bioti...

Considerable Nanoarchaeota novelty and diversity were encountered in Yellowstone Lake, Yellowstone National Park (YNP), where sampling targeted lake floor hydrothermal vent fluids, streamers and sediments associated with these vents, and in planktonic photic zones in three different regions of the lake. Significant homonucleotide repeats (HR) were...

In situ amendments are a promising approach to enhance removal of metal contaminants from diverse environments including soil, groundwater and sediments. Apatite and chitin were selected and tested for copper, chromium, and zinc metal removal in marine sediment samples. Microbiological, molecular biological and chemical analyses were applied to inv...

Little is known about the bioaccumulation dynamics, biotransformation processes, or subsequent toxicity to consumers of dissolved selenite (SeO3) versus selenate (SeO4) uptake into aquatic primary producer communities. To address these data gaps we examined SeO3 and SeO4 bioconcentration into complex freshwater periphyton communities under static a...

Estuaries are among the most productive and dynamic aquatic ecosystems on earth, due to the mixing of fresh and salt waters and significant recycling of nutrients and organic matters. Sitting in a transitional zone, bacterial communities in an estuary typically harbor representatives of both freshwater and marine groups: Alphaproteobacteria, Betapr...

We report the development of microbial populations and changes in their electrochemical production during a 2-month study of a two-chamber microbial fuel cell (MFC). The original inoculum was taken from anaerobic enrichment cultures with soil as the inoculum, and lactate as the exogenous electron donor. Power density (PD), coulombic production (CP)...

Approximately 1200-2000 petagrams (Pg-1015 g) of carbon are stored in the Earth's soil as soil organic matter (SOM), representing two times the amount of carbon stored in the Earth's vegetation and atmosphere combined. SOM significantly influences several essential ecosystem services including nutrient cycling, mitigation of soil erosion, and stora...