scholarly journals Phenanthrene contamination and ploidy level influence the rhizosphere microbiome of Spartina

2019 ◽  
Author(s):  
Armand Cavé-Radet ◽  
Cécile Monard ◽  
Abdelhak El-Amrani ◽  
Armel Salmon ◽  
Malika Ainouche ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Rhizosphere Soil ◽  
Oil Spills ◽  
Its Region ◽  
Hydrocarbon Contamination ◽  
Rrna Gene ◽  
Salt Marsh Plants ◽  
Rhizosphere Microbiome ◽  
Contamination Events

AbstractSpartina spp. are widely distributed salt marsh plants that have a recent history of hybridization and polyploidization. These evolutionary events have resulted in species with a heightened resilience to hydrocarbon contamination, which could make them an ideal model plant for the phytoremediation/reclamation of contaminated coastal ecosystems. However, it is still unknown if allopolyploidization events also resulted in differences in the plant rhizosphere-associated microbial communities, and if this could improve the plant phytoremediation potential. Here, we grew two parental Spartina species, their hybrid and the resulting allopolyploid in salt marsh sediments that were contaminated or not with phenanthrene, a model tricyclic PAH. The DNA from the rhizosphere soil was extracted and the bacterial 16S rRNA gene and ITS region were amplified and sequenced. Generally, both the presence of phenanthrene and the identity of the plant species had significant influences on the bacterial and fungal community structure, composition and diversity. In particular, the allopolyploid S. anglica, harbored a more diverse bacterial community in its rhizosphere, and relatively higher abundance of various bacterial and fungal taxa. Putative hydrocarbon degraders were significantly more abundant in the rhizosphere soil contaminated with phenanthrene, with the Nocardia genus being significantly more abundant in the rhizosphere of S. anglica. Overall our results are showing that the recent polyploidization events in the Spartina did influence the rhizosphere microbiome, both under normal and contaminated conditions, but more work will be necessary to confirm if these differences result in a higher phytoremediation potential.ImportanceSalt marshes are at the forefront of coastal contamination events caused by marine oil spills. Microbes in these environments play a key role in the natural attenuation of these contamination events, often in association with plant roots. One such plant is the Spartina, which are widely distributed salt marsh plants. Intriguingly, some species of the Spartina show heightened resistance to contamination, which we hypothesized to be due to differences in their microbiota. This was indeed the case, with the most resistant Spartina also showing the most different microbiota. A better understanding of the relationships between the Spartina and their microbiota could improve the coastal oil spill clean-up strategies and provide green alternatives to more traditional physico-chemical approaches.

scholarly journals Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Daniel R. Leadbeater ◽  
Nicola C. Oates ◽  
Joseph P. Bennett ◽  
Yi Li ◽  
Adam A. Dowle ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Molecular Mechanisms ◽  
Surface Sediments ◽  
Gene Profiling ◽  
Oxidative Enzymes ◽  
Lignocellulose Degradation ◽  
Rrna Gene ◽  
Enzymatic Mechanisms

Abstract Background Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. Results Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. Conclusions Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments.

scholarly journals Relative and quantitative rhizosphere microbiome profiling result in distinct abundance patterns

2021 ◽  
Author(s):  
Hamed Azarbad ◽  
Julien Tremblay ◽  
Luke D. Bainard ◽  
Etienne Yergeau
Keyword(s):  
Water Stress ◽  
Relative Abundance ◽  
Its Region ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Real Time Quantitative Pcr ◽  
Rhizosphere Microbiome ◽  
History Of ◽  
Almost All

AbstractNext-generation sequencing is recognized as one of the most popular and cost-effective way of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are inherently limited, as they are often presented based on the relative abundance of microbial taxa, which may not fully represent actual microbiome profiles. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that the increase in relative abundance of major microbial phyla does not necessarily result in an increase in abundance. One striking observation when comparing relative and quantitative abundances was a substantial increase in the abundance of almost all phyla associated with the rhizosphere of plants grown in soil with no history of water stress as compared with the rhizosphere of plants growing in soil with a history of water stress, which was in contradiction with the trends observed in the relative abundance data. Our results suggest that the estimated absolute abundance approach gives a different perspective than the relative abundance approach, providing complementary information that helps to better understand the rhizosphere microbiome.

Impact of sea level change on coastal soil organic matter, priming effects and prokaryotic community assembly

2019 ◽  
Vol 95 (10) ◽  
Author(s):  
Thomas Dinter ◽  
Simone Geihser ◽  
Matthias Gube ◽  
Rolf Daniel ◽  
Yakov Kuzyakov
Keyword(s):  
Organic Matter ◽  
Salt Marsh ◽  
Soil Organic Matter ◽  
Salt Marshes ◽  
Extracellular Enzymes ◽  
Rrna Gene ◽  
Co2 Efflux ◽  
Prokaryotic Community ◽  
Priming Effects ◽  
Niche Adaptation

ABSTRACT Salt marshes are coastal areas storing high amounts of soil organic matter (SOM) while simultaneously being prone to tidal changes. Here, SOM-decomposition and accompanied priming effects (PE), which describe interactions between labile and old SOM, were studied under controlled flooding conditions. Soil samples from two Wadden Sea salt marsh zones, pioneer (Pio), flooded two times/day, and lower salt marsh (Low), flooded ∼eight times/month, were measured for 56 days concerning CO2-efflux and prokaryotic community shifts during three different inundation-treatments: total-drained (Drained), all-time-flooded (Waterlogged) or temporal-flooding (Tidal). Priming was induced by 14C-glucose addition. CO2-efflux from soil followed Low>Pio and Tidal>Drained>Waterlogged, likely due to O2-depletion and moisture maintenance, two key factors governed by tidal inundation with regard to SOM mineralisation. PEs in both zones were positive (Drained) or absent (Waterlogged, Tidal), presumably as a result of prokaryotes switching from production of extracellular enzymes to direct incorporation of labile C. A doubled amount of prokaryotic biomass in Low compared to Pio probably induced higher chances of cometabolic effects and higher PE. 16S-rRNA-gene-amplicon-based analysis revealed differences in bacterial and archaeal community composition between both zones, revealing temporal niche adaptation with flooding treatment. Strongest alterations were found in Drained, likely due to inundation-mediated changes in C-binding capacities.

scholarly journals Isolation and Characterization of Polycyclic Aromatic Hydrocarbon-Degrading Bacteria Associated with the Rhizosphere of Salt Marsh Plants

2001 ◽  
Vol 67 (6) ◽  
pp. 2683-2691 ◽  
Author(s):  
L. L. Daane ◽  
I. Harjono ◽  
G. J. Zylstra ◽  
M. M. Häggblom
Keyword(s):  
Salt Marsh ◽  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Rrna Gene ◽  
Gram Positive ◽  
Salt Marsh Plants ◽  
Pah Degradation ◽  
Isolation And Characterization ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic

ABSTRACT Polycyclic aromatic hydrocarbon (PAH)-degrading bacteria were isolated from contaminated estuarine sediment and salt marsh rhizosphere by enrichment using either naphthalene, phenanthrene, or biphenyl as the sole source of carbon and energy. Pasteurization of samples prior to enrichment resulted in isolation of gram-positive, spore-forming bacteria. The isolates were characterized using a variety of phenotypic, morphologic, and molecular properties. Identification of the isolates based on their fatty acid profiles and partial 16S rRNA gene sequences assigned them to three main bacterial groups: gram-negative pseudomonads; gram-positive, non-spore-forming nocardioforms; and the gram-positive, spore-forming group,Paenibacillus. Genomic digest patterns of all isolates were used to determine unique isolates, and representatives from each bacterial group were chosen for further investigation. Southern hybridization was performed using genes for PAH degradation fromPseudomonas putida NCIB 9816-4, Comamonas testosteroni GZ42, Sphingomonas yanoikuyae B1, andMycobacterium sp. strain PY01. None of the isolates from the three groups showed homology to the B1 genes, only two nocardioform isolates showed homology to the PY01 genes, and only members of the pseudomonad group showed homology to the NCIB 9816-4 or GZ42 probes. The Paenibacillus isolates showed no homology to any of the tested gene probes, indicating the possibility of novel genes for PAH degradation. Pure culture substrate utilization experiments using several selected isolates from each of the three groups showed that the phenanthrene-enriched isolates are able to utilize a greater number of PAHs than are the naphthalene-enriched isolates. Inoculating two of the gram-positive isolates to a marine sediment slurry spiked with a mixture of PAHs (naphthalene, fluorene, phenanthrene, and pyrene) and biphenyl resulted in rapid transformation of pyrene, in addition to the two- and three-ringed PAHs and biphenyl. This study indicates that the rhizosphere of salt marsh plants contains a diverse population of PAH-degrading bacteria, and the use of plant-associated microorganisms has the potential for bioremediation of contaminated sediments.

scholarly journals Plant Growth Modifications Due to Coastal Embankments Affect Soil Bacterial and Archaeal Communities Over the Growing Season in Salt Marshes of Eastern China

2022 ◽  
Author(s):  
Hongyu Feng ◽  
Yajun Qiao ◽  
Lu Xia ◽  
Wen Yang ◽  
Yongqiang Zhao ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Diversity ◽  
Soil Properties ◽  
Salt Marshes ◽  
Soil Nutrient ◽  
Rrna Gene ◽  
Organic C ◽  
Bacterial And Archaeal Communities ◽  
Soil Bacterial ◽  
Archaeal Communities

Abstract Aims: Although the influences of coastal embankments on physicochemical soil properties and carbon (C) and nitrogen (N) cycling have been widely studied, the mechanisms of their effects on soil microbial ecologies remain poorly understood. Thus, the aim of this study was to investigate variations in the diversity and composition of soil bacterial and archaeal communities between natural and embanked saltmarshes, as well as the determinants that drive these variations.Methods: 16S rRNA gene sequence analysis was performed to assess the impacts of embankments on the bacterial and archaeal communities of native Suaeda salsa, Phragmites australis, and invasive Spartina alterniflora saltmarshes on the east coast of China.Results: Embankments were found to significantly decrease the microbial diversity of the S. alterniflora salt marsh, while they increased the OTU richness of the P. australis salt marsh. Embankments modified the compositions of soil bacterial and archaeal communities in both the S. alterniflora and P. australis salt marshes. However, variations in the microbial diversity, richness, and community compositions between the native and embanked S. salsa salt marshes were insignificant. Conclusions: These results were possibly because the embankment significantly altered soil nutrient substrate levels (e.g., soil organic C and N) by variations in plant residues and physiochemical soil properties in S. alterniflora and P. australis saltmarshes, whereas the embankment had no observable changes in the soil nutrient substrate and the plant residue in S. salsa saltmarsh. This study also elucidated the effects of coastal embankments on biogeochemical cycles, and highlighted their potential hazards to ecosystems.

Uptake of arsenic by Aster tripolium in relation to rhizosphere oxidation

1991 ◽  
Vol 69 (12) ◽  
pp. 2670-2677 ◽  
Author(s):  
M. L. Otte ◽  
I. M. J. Dekkers ◽  
J. Rozema ◽  
R. A. Broekman
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Bulk Soil ◽  
Marsh Soil ◽  
Salt Marsh Plants ◽  
Aster Tripolium ◽  
Detoxification Mechanism ◽  
Key Factor ◽  
Salt Marsh Soil ◽  
Reduced State

Arsenic present in salt marsh soil is taken up by plants and subsequently transferred to other parts of the ecosystem. The reduced state of the bulk soil of salt marshes favours the mobility of arsenic. In the rhizosphere of plants however, arsenic may be immobilized owing to oxidation of arsenic (III) to less mobile arsenic (V) and adsorption to iron (hydr-)oxides. In a field survey iron concentrations in the vicinity of roots of Aster tripolium were higher than in the bulk soil. In a greenhouse experiment accumulation of arsenic and iron in the rhizosphere occurred, which could be due to the oxidizing activity of plant roots and (or) microorganisms. This process stimulates uptake of arsenic by salt marsh plants. The formation of an iron plaque seems to play an important role in the uptake of arsenic by salt marsh plants, as was indicated by an incubation experiment with root parts of A. tripolium. The results of the experiments indicate that iron plays a key factor in determining the mobility of arsenic in salt marsh soils and in the uptake and translocation processes in the plants. Although oxidation processes in the rhizosphere enhance uptake of arsenic, it may be an important detoxification mechanism for the plants. Key words: arsenic, Aster tripolium, iron, rhizosphere, salt marsh.

BIOLOGICAL CRITERIA FOR THE SELECTION OF CLEANUP TECHNIQUES IN SALT MARSHES

1977 ◽  
Vol 1977 (1) ◽  
pp. 229-235 ◽  
Author(s):  
Barbara Westree
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Oil Spills ◽  
State Of The Art ◽  
The United States ◽  
Physical Characteristics ◽  
Biological Features ◽  
Biological Criteria ◽  
And Behavior ◽  
Selection Of

ABSTRACT During the removal of oil spills in salt marshes, intensive application of manpower and/or equipment may result in physical abuse and injury to the salt marsh far in excess of that caused by the oil itself. Physical characteristics of a salt marsh dictate the distribution and behavior of oil in the marsh. The salt marshes of the United States were grouped into categories based on their physical characteristics. The biological features of each marsh category most sensitive to oil contamination and state-of-the-art cleanup technology were identified. Types and degrees of effect of oils were similarly categorized. Techniques for cleanup were compared to the behavior of uncontained oil in the marsh and the potential for damage evaluated. Degrees of damage were compared and least damaging cleanup strategies selected.

scholarly journals Importance of Biotic and Soil Factors in Determining the Distribution Strategies of Coastal Salt Marsh Plants

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Dong-Ho Son ◽  
Jeom-Sook Lee ◽  
Da Eun Kim ◽  
Seung Ho Lee ◽  
Sun-Kee Hong ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Plant Communities ◽  
Salt Marshes ◽  
Imperata Cylindrica ◽  
Distribution Model ◽  
Group Factor ◽  
Salicornia Europaea ◽  
Relative Significance ◽  
Salt Marsh Plants ◽  
Coastal Salt Marsh

The distribution of plant communities in the salt marshes of the southwestern coasts of South Korea was studied, along with environmental or plant factors, by canonical correspondence analysis (CCA) and the competitor (C), stress tolerator (S), and ruderal (R) (CSR) ecological strategies. The coastal salt-marsh plants were classified into three plant-factor groups in the CCA biplot diagram. Group 1 was correlated with LS and FP. Group 2 was correlated with CH and SLA, and Group 3 was correlated with LA, LDMC and LDW. The salt-marsh plants were classified into four soil-factor groups in the CCA biplot diagram. First, the group factor was correlated with TN, TOC, and Ca2+. Second, the group factor was distributed according to Mg2+, soil texture as Clay and Silt. Third, the group factor was distributed according to Salinity and Na+ content. Fourth, the group factor was distributed according to Sand content. To clarify the relative significance of competition, stress, and disturbance in the distribution process of plant communities, the CSR distribution model was adopted. The nine species showed CR (competitor-ruderal) strategies: Artemisia fukudo, Artemisia scoparis, Aster tripolium, Atriplex gmelinii, Imperata cylindrica var. koenigii, Salicornia europaea, Suaeda japonica, and Suaeda maritima. The four species with C (competitor) strategies were Artemisia capillaris, Limonium tetragonum, Triglochin maritimum, and Zoysia sinica. Carex scabrifolia and Phragmites communis displayed SC (stress-tolerant-competitor). Both distribution patterns of the CCA diagrams and CSR triangles may provide a useful scientific basis for protecting and restoring salt marshes and their valuable ecosystem services, considering the increasing disturbances.

Urbanization impacts on production and recruitment of Fundulus heteroclitus in salt marsh creeks

2020 ◽  
Vol 645 ◽  
pp. 187-204
Author(s):  
PJ Rudershausen ◽  
JA Buckel
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Fundulus Heteroclitus ◽  
Multiple Factor Analysis ◽  
Southeastern Usa ◽  
Density Dependent ◽  
Dependent Relationship ◽  
Juvenile Abundance ◽  
The Relationship ◽  
Throw Trap

It is unclear how urbanization affects secondary biological production in estuaries in the southeastern USA. We estimated production of larval/juvenile Fundulus heteroclitus in salt marsh areas of North Carolina tidal creeks and tested for factors influencing production. F. heteroclitus were collected with a throw trap in salt marshes of 5 creeks subjected to a range of urbanization intensities. Multiple factor analysis (MFA) was used to reduce dimensionality of habitat and urbanization effects in the creeks and their watersheds. Production was then related to the first 2 dimensions of the MFA, month, and year. Lastly, we determined the relationship between creek-wide larval/juvenile production and abundance from spring and abundance of adults from autumn of the same year. Production in marsh (g m-2 d-1) varied between years and was negatively related to the MFA dimension that indexed salt marsh; higher rates of production were related to creeks with higher percentages of marsh. An asymptotic relationship was found between abundance of adults and creek-wide production of larvae/juveniles and an even stronger density-dependent relationship was found between abundance of adults and creek-wide larval/juvenile abundance. Results demonstrate (1) the ability of F. heteroclitus to maintain production within salt marsh in creeks with a lesser percentage of marsh as long as this habitat is not removed altogether and (2) a density-dependent link between age-0 production/abundance and subsequent adult recruitment. Given the relationship between production and marsh area, natural resource agencies should consider impacts of development on production when permitting construction in the southeastern USA.

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