Colin R. Jackson

University of Mississippi | UM · Department of Biology

As sea level rise impacts coastal wetlands, saltmarsh will overtake coastal freshwater marsh in many areas, but changes in the sediment microbiome in response to saltwater intrusion are difficult to predict. Coastal freshwater marsh sediment was exposed to ambient, brackish, and saline conditions as well as to elevated nitrate and phosphate to mode...

Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. Our objective was to unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pip...

Brines at or near the surface of present-day Mars are a potential explanation for seasonally recurring dark streaks on the walls of craters, termed recurring slope lineae (RSL). Deliquescence and freezing point depression are possible drivers of brine stability, attributable to the high salinity observed in martian regolith including chlorides and...

Research on the microbiomes of animals has increased substantially within the past decades. More recently, microbial analyses of aquatic invertebrates have become of increased interest. The storage method used while collecting aquatic invertebrates has not been standardized throughout the scientific community, and the effects of common storage meth...

The Asian clam Corbicula fluminea (Family: Cyneridae) has aggressively invaded freshwater habitats worldwide, resulting in dramatic ecological changes and declines of native bivalves such as freshwater mussels (Family: Unionidae), one of the most imperiled faunal groups. Despite increases in our knowledge of invasive C. fluminea biology, little is...

Freshwater mussels are important for nutrient cycling and ecosystem health as they filter feed on their surrounding water. This filter feeding makes these bivalves especially sensitive to conditions in their environment. Gut microbial communities (microbiomes) have been recognised as important to both host organism and ecosystem health; however, ho...

Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inh...

Background Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from the classification and downstream analyses of traditional operational taxonomic units (OTUs), and towards the usage of amplicon sequence variants (ASVs). While ASVs have several...

Freshwater mussels perform essential ecosystem functions, yet we have no information on how their microbiomes fluctuate over time. In this study, we examined temporal variation in the microbiome of six mussel species (Lampsilis ornata, Obovaria unicolor, Elliptio arca, Fusconaia cerina, Cyclonaias asperata, and Tritogonia verrucosa) sampled from th...

Phyllosphere microorganisms are sensitive to fluctuations in wind, temperature, solar radiation, and rain. However, recent explorations of patterns in phyllosphere communities across time often focus on seasonal shifts and leaf senescence without measuring the contribution of environmental drivers and leaf traits. Here, we focus on the effects of r...

As commodity virtual reality (VR) systems become more common, they are rapidly gaining popularity for entertainment, education, and training purposes. VR utilizes headsets which come in contact with or close proximity to the user's eyes, nose, and forehead. In this study, the potential for these headsets to become contaminated with bacteria was ana...

The bacterial microbiome is an essential component of many corals, although knowledge of the microbiomes in scleractinian corals far exceeds that for octocorals. This study characterized the bacterial communities present in shallow water Caribbean gorgonian octocorals over time and space, in addition to determining the bacterial assemblages in gorg...

Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region...

Rivers are characterized by rapid and continuous one-way directional fluxes of flowing, aqueous habitat, chemicals, suspended particles, and resident plankton. Therefore, at any particular location in such systems there is the potential for continuous, and possibly abrupt, changes in diversity and metabolic activities of suspended biota. As microor...

Freshwater mussels are a species-rich group of aquatic invertebrates that are among the most endangered groups of fauna worldwide. As filter-feeders that are constantly exposed to new microbial inoculants, mussels represent an ideal system to investigate the effects of species or the environment on gut microbiome composition. In this study, we exam...

Research supports the theory that the microbiome of plants and mushrooms produce potent activators of pathogen recognition receptors which are principal contributors to the stimulation of macrophages. We have previously reported that the in vitro macrophage stimulatory activity of water-soluble extracts from 13 different types of edible mushrooms i...

The effect of rain on the phyllosphere community has not been extensively explored, especially in the context of spatial variation on the impact of rain throughout the tree canopy. We characterized the response of the phyllosphere bacterial community removed from leaf surfaces of the Southern Magnolia (Magnolia grandiflora) to rain across different...

Abstract We previously demonstrated that extracts from Echinacea purpurea material varied substantially in their ability to activate macrophages in vitro and that this variation was due to differences in their content of bacterial components. The purpose of the current study was to identify soil conditions (organic matter, nitrogen, and moisture co...

Common ecological restoration treatments such as thinning trees and prescribed burning could result in changes to soil fungal communities and changes to the function of those communities. Ecto-mycorrhizal fungi are especially likely to be affected as they are symbionts on plant roots and exhibit host and niche preferences. Ectomycorrhizal fungi als...

The above‐ground surfaces of plants (the phyllosphere) harbour a diverse variety of microorganisms, and this phyllosphere microbiome interacts with the host plant affecting its health and function. Phyllosphere microorganisms, predominantly bacteria and fungi, can act as mutualists promoting plant growth and tolerance of environmental stressors, co...

The above-ground surfaces of plants (the phyllosphere) harbour a diverse variety of microorganisms, and this phyllosphere microbiome interacts with the host plant affecting its health and function. Phyllosphere microorganisms, predominantly bacteria and fungi, can act as mutualists promoting plant growth and tolerance of environmental stressors, co...

We examined the downriver patterns of variation in taxonomic diversity of the Mississippi River bacterioplankton microbiome along 1,300 river kilometers, or approximately one third the total length of the river. The study section included portions of the Upper, Middle, and Lower Mississippi River, confluences with five tributaries draining distinct...

The Mississippi River drainage basin includes the Illinois, Missouri, Ohio, Tennessee, and Arkansas rivers. These rivers drain areas with different physiography, population centers, and land use, with each contributing a different suites of metals and wastewater contaminants that can affect water quality. In July 2012, we determined 18 elements (Be...

In the Caribbean, gorgonian corals dominate many coral reefs, while scleractinian coral cover has declined. Gorgonian corals deal with stressors such as lesions caused by wave action, predation, or human activities. In June 2012, artificial wounds were inflicted on branches of the gorgonians Eunicea flexuosa and Pseu- doplexaura porosa found at 3–5...

Understanding methane emissions from natural sources is becoming increasingly important with future climactic uncertainty. Wetlands are the single largest natural source of methane; however, little attention has been given to how biota, and interactions between above and belowground communities may affect methane emission rates in these systems. To...

Plant-mediated transport is the dominant means of methane release from vegetated wetlands. Whether aboveground plant disturbances affect the emission of methane is largely unknown. We tested the effects of stem clipping on methane emissions from freshwater wetland mesocosms vegetated with Sagittaria lancifolia, Panicum hemitomon, Echinochloa walter...

Recent studies have indicated that a major contributor to the innate immune enhancing properties of some medicinal plants is derived from the cell wall components of bacteria colonizing these plants. The purpose of the current study was to assess if the bacteria present within edible and medicinal mushrooms substantially contribute to the innate im...

Saltmarshes are typically dominated by perennial grasses with large underground rhizome systems that can change local sediment conditions and be important in shaping the sediment microbial community. Factors such as salinity that control plant zonation in saltmarshes are also likely to influence the microbial community, but little is known as to wh...

Evidence supports the theory that bacterial communities colonizing Echinacea purpurea contribute to the innate immune enhancing activity of this botanical. Previously, we reported that only about half of the variation in in vitro monocyte stimulating activity exhibited by E. purpurea extracts could be accounted for by total bacterial load within th...

Vertebrates harbor microbes both internally and externally, and collectively these microorganisms (the "microbiome") contain genes that outnumber the host's genetic information ten-fold. The majority of the microorganisms associated with vertebrates are found within the gut; where they influence host physiology, immunity, and development. The devel...

The phyllosphere presents a unique system of discrete and easily replicable surfaces colonized primarily by bacteria. However, the biogeography of bacteria in the phyllosphere is little understood, especially at small to intermediate scales. Bacterial communities on the leaves of 91 southern magnolia (Magnolia grandiflora) trees 1-452 m apart in a...

Extracellular enzymes degrade macromolecules into soluble substrates and are important for nutrient cycling in soils, where microorganisms, such as ectomycorrhizal (ECM) fungi, produce these enzymes to obtain nutrients. Ecotones between forests and fields represent intriguing arenas for examining the effect of the environment on ECM community struc...

Vertebrates are metagenomic organisms in that they are composed not only of their own genes but also those of their associated microbial cells. The majority of these associated microorganisms are found in the gastrointestinal tract (GIT) and presumably assist in processes such as energy and nutrient acquisition. Few studies have investigated the as...

Plants harbor a diverse microbiome existing as bacterial populations on the leaf surface (the phyllosphere) and within plant tissues (endophytes). The composition of this microbiome has been largely unexplored in fresh produce vegetables, where studies have tended to focus on pathogen detection and survival. However, the application of next-generat...

Microbial extracellular enzyme activity is responsible for much of the carbon and nutrient cycling in freshwaters, and logically there should a relationship between the chemical properties of a system and its enzymatic profile. To evaluate this concept, we surveyed extracellular enzyme activity in five large rivers (the Upper Mississippi, Missouri,...

A growing body of evidence suggests that endophytic bacteria within Echinacea are the main source of components responsible for enhancing innate immune function in vitro and in vivo. We have found that 97% of in vitro monocyte/macrophage activation by extracts of Echinacea and other immune enhancing botanicals is due to the bacterial components LPS...

Previous studies from our laboratory indicate that LPS and Braun type lipoproteins derived from endophytic bacteria within Echinacea are responsible for 97% of in vitro monocyte/macrophage activation by extracts of this botanical. Furthermore, we have found that changes in the levels of these two components are responsible for the variation (˜100-f...

The different drainage basins of large rivers such as the Mississippi River represent interesting systems in which to study patterns in freshwater microbial biogeography. Spatial variability in bacterioplankton communities in six major rivers (the Upper Mississippi, Missouri, Illinois, Ohio, Tennessee, and Arkansas) of the Mississippi River Basin w...

Background/Question/Methods Decomposition of leaf litter is a critical process in the cycling of nutrients through forest ecosystems. In the interior southern U.S., open oak woodlands were once common, and were adapted to and maintained by fire. However, over a century of fire suppression has allowed the growth of fire sensitive and shade toleran...

Background/Question/Methods North Mississippi uplands were historically maintained as open oak or oak-pine woodlands through frequent fire. After a period of fire suppression beginning in the 1920s led to a closed canopy, thinning and prescribed fire are now being used to create suitable habitat for fire-dependent plant and animal species. A key...

We have previously reported that over 97% of in vitro monocyte/macrophage activation by botanical plant extracts was due to bacterial components (LPS and Braun type lipoproteins). Furthermore, we have also shown that in Echinacea purpurea total bacterial load was significantly correlated with macrophage activity and LPS content. The objective of th...

We have found that the bacterial components lipopolysaccharides (LPS) and Braun-type lipoproteins are responsible for the majority of the in vitro macrophage activation exhibited by extracts of Echinacea and other immune enhancing botanicals. Furthermore, we show that endophytic bacteria are the principal source of these components. We also show th...

Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally...

Much of the nutrient cycling and carbon processing in natural environments occurs through the activity of extracellular enzymes released by microorganisms. Thus, measurement of the activity of these extracellular enzymes can give insights into the rates of ecosystem level processes, such as organic matter decomposition or nitrogen and phosphorus mi...

Background/Question/Methods Present day concentrations of methane (CH4) in the atmosphere are unprecedented throughout the past 420,000 years of our planet. This poses a threat to environmental stability because of the power of CH4 to alter climactic patterns. Wetland ecosystems are the largest natural source of global atmospheric CH4 emission, em...

Passage of agricultural runoff through vegetated drainage ditches has been shown to reduce the amount of pesticides, such as atrazine, exiting out of agricultural watersheds. Previous studies have found that microbial communities in soil from fields treated with atrazine display enhanced rates of atrazine degradation. However, no studies have exami...

Microorganisms play important roles in wetland ecosystems, but little is known about the influence of wetland plants on microbial community structure and activity. A greenhouse experiment was conducted to study the short-term influence of wetland vegetation on the sediment microbial community. Mesocosms were either planted with Juncus effusus, Care...

We have found that the bacterial components lipopolysaccharides (LPS) and Braun-type lipoproteins are responsible for the majority of the in vitro macrophage activation exhibited by extracts of Echinacea and other immune enhancing botanicals. Furthermore, we show that endophytic bacteria are the principal source of these components. We also show th...

Our previous studies indicate that the majority of in vitro monocyte/macrophage activation exhibited by extracts of Echinacea depends on bacterial components. In the present study, total bacterial load was determined within E. purpurea samples and ranged from 6.4 × 106 to 3.3 × 108 bacteria/g of dry plant material. To estimate total bacterial load,...

Background/Question/Methods Increasing carbon dioxidein our atmosphere due to anthropogenic factors has led to an increased interest in the ability of ecosystems to act as carbon sinks. Ectomycorrhizal fungi (EMF) are symbionts of trees and link plants to soil carbon pools. Understanding the role that EMF play in soil carbon storage could provide...

The phyllosphere contains a diverse bacterial community that can be intimately associated with the host plant; however, few studies have examined how the phyllosphere community changes over time. We sampled replicate leaves from a single magnolia (Magnolia grandiflora) tree in the winter of three consecutive years (2007-2009) as well as during four...

Biochemical conversion of lignocellulosic biomass to ethanol involves size reduction, preprocessing, pretreatment, enzyme hydrolysis, and fermentation. In recent years, microbial preprocessing has been gaining attention as a means to produce labile biomass for lessening the requirement of pretreatment severity. However, loss of sugars due to microb...

Background/Question/Methods Fire has been an integral part of the natural history of North American forests as a natural disturbance that shapes community composition and ecosystem function. Organized fire suppression beginning in the early 20th century has converted historically fire-tolerant oak dominated ecosystems of the eastern United States...

Peat swamp forests are found in tropical lowlands, primarily in Southeast Asia, where high rainfall and poor drainage conditions combine to slow organic matter decomposition rates and result in the accumulation of deep layers of peat. They differ from temperate peatlands in that they are covered with tropical rainforest rather than herbaceous veget...

In situ decomposition of above and belowground plant biomass of the native grass species Andropogon glomeratus (Walt.) B.S.P. and exotic Imperata cylindrica (L.) Beauv. (cogongrass) was investigated using litter bags over the course of a 12month period. The above and belowground biomass of the invasive I. cylindrica always decomposed faster than th...

Microorganisms mediate the decomposition of leaf-litter through the release of extracellular enzymes. The surfaces of decomposing leaves are both chemically and physically heterogeneous, and spatial patterns in microbial enzyme activity on the litter surface should provide insights into fine-scale patterns of leaf-litter decomposition. Platanus occ...

To evaluate the effects of saltwater intrusion and nutrient enrichment on wetland microbial communities, we measured changes in sediment microbial structure and function in response to increased salinity and nutrients. Sediments were collected from a cypress-tupelo swamp near Lake Pontchartrain, Louisiana, USA, and maintained in microcosms treated...

Bacterial communities associated with sediment particles were examined using PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. Particle size influenced community structure, with attached bacterial assemblages separating into 63- to 125-, 125- to 1,000-, and 1,000- to 2,000-μm fractions. Differences were particularly pronounc...

Tropical peat swamp forests are important and endangered ecosystems, although little is known of their microbial diversity and ecology. We used molecular and enzymatic techniques to examine patterns in prokaryotic community structure and overall microbial activity at 0-, 10-, 20-, and 50-cm depths in sediments in a peat swamp forest in Malaysia. De...

1. We review studies of viruses in natural and constructed wetlands, focusing on the importance of surfaces as viral habitat, and differences in viral ecology between wetlands and other aquatic ecosystems. 2. Viruses in natural wetlands are predominantly associated with sediment, macrophytes and other submerged surfaces. In constructed wetlands, th...

Molecular and biochemical approaches have revealed that microbial communities in natural aquatic environments are more diverse than previously thought. However, few studies have examined how fine scale changes in environmental conditions can alter the structure, diversity, and function of aquatic microorganisms. We performed a number of studies tha...