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.

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 Correction: Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling

PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0204600
Author(s):  
Renee M. Petri ◽  
Poulad Pourazad ◽  
Ratchaneewan Khiaosa-ard ◽  
Fenja Klevenhusen ◽  
Barbara U. Metzler-Zebeli ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Temporal Dynamics ◽  
Gene Profiling ◽  
Rrna Gene

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.

Long-Term Effects of an Oil Spill on Populations of the Salt-Marsh Crab Uca pugnax

1978 ◽  
Vol 35 (5) ◽  
pp. 648-649 ◽  
Author(s):  
C. T. Krebs ◽  
K. A. Burns
Keyword(s):  
Salt Marsh ◽  
Oil Spill ◽  
Salt Marshes ◽  
Surface Sediments ◽  
Fuel Oil ◽  
Long Term Effects ◽  
Uca Pugnax ◽  
Crab Population ◽  
Body Tissues

A spill of fuel oil at West Falmouth, Massachusetts, in 1969 contaminated contiguous salt marshes with up to 6000 μg oil/g (ppm) of wet mud and affected local populations of the salt-marsh crab Uca pugnax. Directly related to high sediment oil content were reduced crab density, reduced ratio of females to males, reduced juvenile settlement, heavy overwinter mortality, incorporation of oil into body tissues, behavioral disorders such as locomotor impairment, and abnormal burrow construction. Concentrations of weathered fuel oil > 1000 ppm were directly toxic to adults, while those of 100–200 ppm were toxic to juveniles. Cumulative effects occurred at lower concentrations. Recovery of the marsh from this relatively small oil spill is still incomplete after 7 yr. Interpretation of the crab population data upon the basis of detailed analysis of the aromatic fraction of the fuel oil provided by Dr J. Teal, Woods Hole Oceanographic Institution, showed that recovery of the crab populations was highly correlated with the disappearance of the naphthalene fraction of the aromatics. There had been a decrease in the aromatics from 42% in 1970 to approximately 18% in 1976 in Station I surface sediments, while preliminary analyses show aromatics still high at other stations where little recovery has been observed. By 1970–71 all parent naphthalene compounds were gone in Station I surface sediments, but substituted naphthalenes were still in high concentrations. By 1972–73 dimethyl naphthalenes and C3 and C4 substituted naphthalenes remained at about 25% of original values. By 1976–77 only C3 and C4 substituted naphthalenes remained at less than one tenth of their 1973 levels. In 1972–73 the substituted naphthalenes were at high enough concentrations to prevent recruitment, as large juvenile crab settlements in 1970–73 produced no recruitment into the crab populations. By 1976–77 these toxic compounds were at low enough levels that recovery of the crab population was occurring with recruitment, and increasing density was observed in both years. High aromatic concentrations at other stations may still be inhibiting recovery at these stations. The long-term inhibition of recruitment and low population densities may have resulted from exposure to oil in the interstitial waters during the sensitive molt period and/or during the long periods of time while the crabs were overwintering in the substrate. Key words: petroleum, Uca pugnax, crab, salt-marsh, population, pollution

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.

scholarly journals Biomarker (brGDGT) degradation and production in lacustrine surface sediments: Implications for paleoclimate reconstructions.

2020 ◽  
Author(s):  
Cindy De Jonge ◽  
Annika Fiskal ◽  
Xingguo Han ◽  
Mark Lever
Keyword(s):  
Lake Water ◽  
Surface Sediments ◽  
Rrna Gene ◽  
Temperature Record ◽  
Surficial Sediments ◽  
Temperature Changes ◽  
Reconstructed Temperature ◽  
Paleoclimate Reconstructions ◽  
Long Timescales

<p>Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are a class of biomarker lipids that can be conserved over long timescales in lake sediments. Produced throughout the lake water column before settling and incorporation in the sedimentary archive, they are used to reconstruct lake water temperature changes through time. However, it is not clear how degradation and/or production of these compounds in the surface sediments influences the brGDGT signal and the reconstructed temperature record.</p><p>Here we present the core lipid (“fossil”) and intact polar lipid (“recently produced”) signal of brGDGT lipids in 8 short cores collected in 4 Swiss lakes, covering a eutrophic gradient. In eutrophic conditions (Lake Baldegg), a clear subsurface (20-35 cm blf) maximum in intact polar lipids is observed (15-20%), whereas the most surficial sediments (0-2 cm blf) show the lowest percentage of IPL lipids (<5%). Our data indicates that tetramethylated brGDGT lipids are produced in the subsurface. As the bacterial community has been reconstructed in all cores, using 16S rRNA gene distribution, we observe that this production is coeval with an increase in the relative abundance of OTUs in the phyla Acetothermia, Aminicenantes, Caldiserica and Spirochaetes. Hexamethylated brGDGTs are encountered in increased amounts in most surficial sediments (0-2 cm bsf), but are degraded further downcore. Both degradation and in-situ production cause the reconstructed temperatures based on the surface sediments to be 2 ℃ colder than those from the subsurface.</p><p>In sediments where degradation and subsurface production of brGDGT lipids occurs, this has the potential to impact paleoclimate reconstructions. A colder MBT’<sub>5ME</sub> signal in surface sediments has indeed been observed in several studies (i.e. Tierney et al., 2012; Miller et al., 2018, Martin et al., 2020). Furthermore, a distinct brGDGT signal in surface sediments has a possible impact on existing lacustrine calibration datasets, as these are based on surface sediments.</p><p>References:</p><p>Tierney et al. (2012), GCA 77, p561-581. Miller et al. (2018), CoP 14 (11), p1653-1667. Martin et al. (2020), QSR 228, 106109.</p>

scholarly journals Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling

PLoS ONE ◽  
2017 ◽  
Vol 12 (8) ◽  
pp. e0182271 ◽  
Author(s):  
Renee M. Petri ◽  
Poulad Pourazad ◽  
Ratchaneewan Khiaosa-ard ◽  
Fenja Klevenhusen ◽  
Barbara U. Metzler-Zebeli ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Temporal Dynamics ◽  
Gene Profiling ◽  
Rrna Gene

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.

scholarly journals A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

2020 ◽  
Vol 8 (6) ◽  
pp. 936 ◽  
Author(s):  
Claudia Leoni ◽  
Mariateresa Volpicella ◽  
Bruno Fosso ◽  
Caterina Manzari ◽  
Elisabetta Piancone ◽  
...  
Keyword(s):  
Ecological Model ◽  
Salinity Range ◽  
Rrna Gene ◽  
Hypervariable Regions ◽  
Cell Counts ◽  
Precious Resource ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
The 16S Rrna Gene

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.

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