Hydrodynamic Investigation of Upper Mississippi River Freshwater Mussel Habitats

Young, Nathan; McCo, Andrew; Weber, Larry

doi:10.1061/40792(173)585

Cited by 3 publications

(2 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our study sites were located in the backwaters of the UMR navigation pool 16, where a consistently populated mussel assemblage has been studied for decades ( USACE, 1981 , 1984 ; Young et al, 2005 ; Morales et al, 2006 ). Sediment cores were obtained from the mussel habitat (41.452804, -90.763299) and upstream sediment (41.451540, -90.753275) lacking mussels ( Black et al, 2017 ); both sites had similar hydraulics and sediment composition ( Young et al, 2005 ), and will be considered as treatments “with-mussels” and with “no-mussels” according to previous studies ( Mirto et al, 2000 ; Danovaro et al, 2004 ). Cores were removed from each site using a 2-in diameter, post-driver with a polypropylene liner (Multi-State Sediment Sampler, Art’s Manufacturing and Supply, Inc.; American Falls, ID, United States), and an ethanol flame-sterilized 3/8-in diameter drill bit was used to penetrate the cores at depths of 3 and 5 cm.…”

Section: Methodsmentioning

confidence: 99%

The Genomic Potentials of NOB and Comammox Nitrospira in River Sediment Are Impacted by Native Freshwater Mussels

Black

Just

2018

Front. Microbiol.

View full text Add to dashboard Cite

Freshwater mussel assemblages of the Upper Mississippi River (UMR) sequester tons of ammonia- and urea-based biodeposits each day and aerate sediment through burrowing activities, thus creating a unique niche for nitrogen (N) cycling microorganisms. This study explored how mussels impact the abundance of N-cycling species with an emphasis on Candidatus Nitrospira inopinata, the first microorganism known to completely oxidize ammonia (comammox) to nitrate. This study used metagenomic shotgun sequencing of genomic DNA to compare nitrogen cycling species in sediment under a well-established mussel assemblage and in nearby sediment without mussels. Metagenomic reads were aligned to the prokaryotic RefSeq non-redundant protein database using BLASTx, taxonomic binning was performed using the weighted lowest common ancestor algorithm, and protein-coding genes were categorized by metabolic function using the SEED subsystem. Linear discriminant analysis (LDA) effect sizes were used to determine which metagenomes and metabolic features explained the most differences between the mussel habitat sediment and sediment without mussels. Of the N-cycling species deemed differentially abundant, Nitrospira moscoviensis and “Candidatus Nitrospira inopinata” were responsible for creating a distinctive N-cycling microbiome in the mussel habitat sediment. Further investigation revealed that comammox Nitrospira had a large metabolic potential to degrade mussel biodeposits, as evidenced the top ten percent of protein-coding genes including the cytochrome c-type biogenesis protein required for hydroxylamine oxidation, ammonia monooxygenase, and urea decomposition SEED subsystems. Genetic marker analysis of these two Nitrospira taxons suggested that N. moscoviensis was most impacted by diverse carbon metabolic processes while “Candidatus Nitrospira inopinata” was most distinguished by multidrug efflux proteins (AcrB), NiFe hydrogenase (HypF) used in hydrogen oxidation and sulfur reduction coupled reactions, and a heme chaperone (CcmE). Furthermore, our research suggests that comammox and NOB Nitrospira likely coexisted by utilizing mixotrophic metabolisms. For example, “Candidatus Nitrospira inopinata” had the largest potentials for ammonia oxidation, nitrite reduction with NirK, and hydrogen oxidation, while NOB Nitrospira had the greatest potential for nitrite oxidation, and nitrate reduction possibly coupled with formate oxidation. Overall, our results suggest that this mussel habitat sediment harbors a niche for NOB and comammox Nitrospira, and ultimately impacts N-cycling in backwaters of the UMR.

show abstract

Section: Methodsmentioning

confidence: 99%

The Genomic Potentials of NOB and Comammox Nitrospira in River Sediment Are Impacted by Native Freshwater Mussels

Black

Just

2018

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…Our study sites were located in the backwaters of the Upper Mississippi River navigation pool 16, where a consistently populated mussel assemblage has been studied for decades [44,[240][241][242]. Sediment cores were obtained from the mussel habitat (41.452804, -90.763299) and upstream sediment (41.451540, -90.753275) lacking mussels [203]; both sites had similar hydraulics and sediment composition [240], and will be considered as treatments "with-mussels" and with "no-mussels" according to previous studies [243,244]. Cores were removed from each site using a 2-in diameter, post-driver earlier, selection of these samples were informed by evidence suggesting oxic-anoxic interface niches were located at 5 cm sediment depth without mussels and 3 cm depth beneath mussels [203].…”

Section: Sediment Collection and Dna Isolationmentioning

confidence: 99%

Assessing the impacts of native freshwater mussels on nitrogen cycling microbial communities using metagenomics

Black¹

View full text Add to dashboard Cite

Effects of substrate and hydrodynamic conditions on the formation of mussel beds in a large river

Morales

Weber²,

Mynett

et al. 2006

Journal of the North American Benthological Society

126

116

View full text Add to dashboard Cite

A numerical model for simulation of freshwater mussel dynamics was used to investigate the effects of substrate and hydrodynamic conditions on the formation of mussel beds in a 10-km reach of the Upper Mississippi River (UMR). Suitable habitats for mussel survival were identified by creating a dimensionless parameter (shear stress ratio) combining shear force and substrate type. This parameter is a measure of substrate stability that could be used in many different applications. Dispersal of juvenile mussels with flow as they detach from their fish hosts was simulated by a particle-tracking mechanism that identified suitable areas for colonization with the potential to evolve into mussel beds. Simulated areas of mussel accumulation coincided with reported locations of mussel beds, and simulated densities were in the range of abundant mussel beds in other reaches of the UMR. These results, although more qualitative than quantitative, provide insight into factors influencing the formation of mussel beds in a large river.

show abstract

Hydrodynamic Investigation of Upper Mississippi River Freshwater Mussel Habitats

Cited by 3 publications

References 11 publications

The Genomic Potentials of NOB and Comammox Nitrospira in River Sediment Are Impacted by Native Freshwater Mussels

The Genomic Potentials of NOB and Comammox Nitrospira in River Sediment Are Impacted by Native Freshwater Mussels

Assessing the impacts of native freshwater mussels on nitrogen cycling microbial communities using metagenomics

Effects of substrate and hydrodynamic conditions on the formation of mussel beds in a large river

Contact Info

Product

Resources

About