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

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.

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Alteration of Nutrient Substrates and Absence of Seawater Due to Coastal Embankments Affects Soil Microbial Communities in Salt Marshes of Eastern China

10.21203/rs.3.rs-707097/v1 ◽

2021 ◽

Author(s):

Hongyu Feng ◽

Yajun Qiao ◽

Lu Xia ◽

Wen Yang ◽

Yongqiang Zhao ◽

...

Keyword(s):

Physicochemical Properties ◽

Eastern China ◽

Soil Microbial Communities ◽

Soil Nutrient ◽

Rrna Gene ◽

Soil Physicochemical Properties ◽

Organic C ◽

Soil Microbial ◽

Bacterial And Archaeal Communities ◽

Archaeal Communities

Abstract Aims: Although the influence of coastal embankments on soil physicochemical properties and carbon (C) and nitrogen (N) cycling has been widely studied, the mechanisms of their effects on the soil microbial ecology are still poorly understood. Thus, the aim of this study was to investigate variations in 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 the invasive Spartina alterniflora Loisel., as well as native Suaeda salsa (L.) Pall. and Phragmites australis (Cav.) Trin. ex Steud. saltmarshes in the coastal China.Results: Embankments significantly decreased the Simpson diversity index of the S. alterniflora saltmarsh, while increasing the OTU richness in the P. australis saltmarsh. Additionally, the bacterial and archaeal community compositions in the embanked S. alterniflora and P. australis saltmarshes were considerably modified. However, no variations were found between the bacterial and archaeal communities of the natural and embanked S. salsa saltmarshes.Conclusions: These results were possibly because embankments decreased the soil nutrient substrates (e.g., soil organic C and N) dramatically in the S. alterniflora saltmarsh, while increased soil nutrient substrates significantly in the P. australis saltmarsh. However, embankments had a negligible effect on the soil nutrient substrates in the S. salsa saltmarsh. Moreover, embankments increased the abundance of Betaproteobacteria, and decreased the abundance of sulfur- and sodium-dependent bacteria due to the dramatic change in soil physicochemical properties.

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Long-Term N Fertilization Decreased Diversity and Altered the Composition of Soil Bacterial and Archaeal Communities

Agronomy ◽

10.3390/agronomy9100574 ◽

2019 ◽

Vol 9 (10) ◽

pp. 574 ◽

Cited By ~ 3

Author(s):

Renpeng Sun ◽

Pan Zhang ◽

Chance W. Riggins ◽

María C. Zabaloy ◽

Sandra Rodríguez-Zas ◽

...

Keyword(s):

Crop Production ◽

Soil Microbial Communities ◽

N Fertilization ◽

Rrna Gene ◽

Maize Production ◽

Soil Microbial ◽

Continuous Maize ◽

Bacterial And Archaeal Communities ◽

Soil Bacterial ◽

Archaeal Communities

Soil microbial communities are essential in the cycling of nutrients that affect crop production. Our goal was to characterize the microbial community structure following 34 years of nitrogen (N) fertilization treatments in continuous maize production in highly fertile soils. Using 16S rRNA gene-based analysis of the V4 region via Illumina HiSeq2500 technology with downstream bioinformatics processing and analysis with QIIME 2.0, we aimed to characterize the prokaryotic communities under three increasing N fertilization rates. Factor analyses indicated that a high N level decreased the diversity of soil bacterial and archaeal communities and altered the relative abundance (RA) of the dominant (>1% RA) and minor (<1% RA) phyla. Among the 12 major phyla, we determined increases in Gemmatimonadetes, Proteobacteria, and Euryarchaeota, accompanied by reductions in Cyanobacteria, Chloroflexi, Firmicutes, and Planctomycetes with increasing N. Within the 29 minor phyla, N fertilization led to increases in Aquificae, WPS2, Parvarchaeota, AD3, FCPU426, Armatimonadetes, TM7, Chlamydiae, and OD1, along with reductions of Nitrospirae, WS3, Tenericutes, Lentisphaerae, OP3, Synergistetes, Thermotogae, and prokaryotes that could not be reliably assigned to a phylum (classified as Other).

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

Microbiome ◽

10.1186/s40168-020-00964-0 ◽

2021 ◽

Vol 9 (1) ◽

Cited By ~ 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.

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New insights into the influence of plant and microbial diversity on denitrification rates in a salt marsh

10.1101/2020.08.03.234666 ◽

2020 ◽

Author(s):

Olivia U. Mason ◽

Patrick Chanton ◽

Loren N. Knobbe ◽

Julian Zaugg ◽

Behzad Mortazavi

Keyword(s):

Microbial Community ◽

Salt Marsh ◽

Microbial Diversity ◽

Ecosystem Functions ◽

Juncus Roemerianus ◽

Rrna Gene ◽

Metabolic Potential ◽

Marsh Vegetation ◽

Core Microbiome ◽

N Removal

AbstractCoastal salt marshes are some of the most productive ecosystems on Earth, providing numerous services such as soil carbon storage, flood protection and nutrient filtering, several of which are mediated by the sediment microbiome associated with marsh vegetation. Here, nutrient filtering (nitrate removal through denitrification) was examined by determining microbial community structure (16S rRNA gene iTag sequencing), diversity, denitrification rates and metabolic potential (assembled metagenomic sequences) in collocated patches of Spartina alterniflora (Spartina) and Juncus roemerianus (Juncus) sediments. The iTag data showed that diversity and richness in Spartina and Juncus sediment microbial communities were highly similar. However, microbial community evenness differed significantly, with the most even communities observed in Juncus sediments. Further, denitrification rates were significantly higher in Juncus compared to Spartina, suggesting oscillations in microbial abundances and in particular the core microbiome identified herein, along with plant diversity influence marsh nitrogen (N) removal. Amplicon and assembled metagenome sequences pointed to a potentially important, yet unappreciated Planctomycetes role in N removal in the salt marsh. Thus, perturbations, such as sea-level rise, that can alter marsh vegetation distribution could impact microbial diversity and may ultimately influence the ecologically important ecosystem functions the marsh sediment microbiome provides.

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Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation

Forests ◽

10.3390/f10070550 ◽

2019 ◽

Vol 10 (7) ◽

pp. 550 ◽

Cited By ~ 6

Author(s):

Huili Feng ◽

Jiahuan Guo ◽

Weifeng Wang ◽

Xinzhang Song ◽

Shuiqiang Yu

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Relative Abundance ◽

Rrna Gene ◽

Poplar Plantation ◽

Plantation Forest ◽

Bacterial And Archaeal Communities ◽

Different Depths ◽

Archaeal Communities

Understanding the composition and diversity of soil microorganisms that typically mediate the soil biogeochemical cycle is crucial for estimating greenhouse gas flux and mitigating global changes in plantation forests. Therefore, the objectives of this study were to investigate changes in diversity and relative abundance of bacteria and archaea with soil profiles and the potential factors influencing the vertical differentiation of microbial communities in a poplar plantation. We investigated soil bacterial and archaeal community compositions and diversities by 16S rRNA gene Illumina MiSeq sequencing at different depths of a poplar plantation forest in Chenwei forest farm, Sihong County, Jiangsu, China. More than 882,422 quality-filtered 16S rRNA gene sequences were obtained from 15 samples, corresponding to 34 classified phyla and 68 known classes. Ten major bacterial phyla and two archaeal phyla were found. The diversity of bacterial and archaeal communities decreased with depth of the plantation soil. Analysis of variance (ANOVA) of relative abundance of microbial communities exhibited that Nitrospirae, Verrucomicrobia, Latescibacteria, GAL15, SBR1093, and Euryarchaeota had significant differences at different depths. The transition zone of the community composition between the surface and subsurface occurred at 10–20 cm. Overall, our findings highlighted the importance of depth with regard to the complexity and diversity of microbial community composition in plantation forest soils.

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

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz129 ◽

2019 ◽

Vol 95 (10) ◽

Cited By ~ 4

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.

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Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards

Journal of Zhejiang University SCIENCE B ◽

10.1631/jzus.b1400114 ◽

2014 ◽

Vol 15 (11) ◽

pp. 953-965 ◽

Cited By ~ 5

Author(s):

Hua Wang ◽

Shao-hui Yang ◽

Jing-ping Yang ◽

Ya-min Lv ◽

Xing Zhao ◽

...

Keyword(s):

Temporal Changes ◽

Bacterial And Archaeal Communities ◽

Soil Bacterial ◽

Archaeal Communities

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Drivers and outcomes of salt marsh erosion

10.5194/egusphere-egu2020-20331 ◽

2020 ◽

Author(s):

Andrea D'Alpaos ◽

Marcella Roner ◽

Laura Tommasini ◽

Alvise Finotello ◽

Massimiliano Ghinassi ◽

...

Keyword(s):

Salt Marsh ◽

Soil Properties ◽

Salt Marshes ◽

Wind Waves ◽

Wave Power ◽

Strong Wind ◽

Erosion Rates ◽

Ecological Features ◽

Local Soil ◽

Lateral Erosion

Salt marshes are widespread features of tidal landscapes and exert a primary control on the ecomorphodynamic evolution of these environments, delivering valuable ecosystem services. Among the latter, salt marshes furnish a shoreline buffer between the mainland and the sea, dissipating waves and mitigating erosion during storms, filter nutrients and pollutants, serve as an organic carbon sink, and provide diverse ecological habitats.The sustainability of most of the modern salt-marsh systems worldwide is threatened by increasing anthropogenic pressures, as well as by changes in climate forcings. Particularly, the dramatic decrease in marsh extent, observed worldwide during the last centuries, has long been ascribed to the combined effects of rising relative sea level and sediment starvation. However, even though both those processes may cause the drowning of extensive salt-marsh areas, recent studies have demonstrated that the great majority of salt marshes worldwide are being lost due to the lateral erosion of their margins. If on the one hand the lateral retreat triggered by wind waves is recognized as a primary driver for salt-marsh lateral retreat, on the other hand it still remains questionable whether different local soil properties (e.g., water content, dry bulk density, organic matter content, inorganic grain size) and vegetation cover actively affect the resistance, and ultimately the erosion, of salt-marsh margins.Here we investigate, by means of numerical modelling combined with field and laboratory analyses, how the interplays between incoming wave power, ecological features, and soil properties influence the erosion rates of salt-marsh margins in the Venice lagoon (Italy).We show that lateral erosion rates of salt marshes are primarily controlled by the incoming wind-wave power, mediated by the presence of different halophytes, whereas significant influence of soil properties is observed.Erosion rates are reduced in marsh edges colonized by particular associations of halophytic vegetation species, and along gently sloped and irregular margins facing very shallow tidal flats. Conversely, erosion rates are enhanced in cliffed margins exhibiting smooth planform morphologies, which are typically stricken by strong wind waves.By clarifying the interactions between the dynamics and functional shapes of salt marsh edges, our observations might be valuable for the conservation and restoration of salt-marsh landscapes, especially in the face of a globally changing climate.

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