Mesocosm and Microcosm Experiments On the Feeding of Temperate Salt Marsh Foraminifera

Abstract Agglutinated foraminifera dominate in temperate salt marsh sediment, making them key indicators for monitoring sea level and environmental changes. Little is known about the biology of these benthic foraminifera because of difficulties in distinguishing live from dead specimens in laboratory cultures. We present data from 10 years of laboratory experiments using comparisons of the agglutinant trochamminids Trochammina inflata and Entzia macrescens and the miliolid Miliammina fusca with the calcareous rotalids Helenina anderseni and Elphidium williamsoni. Specimens were taken from a laboratory mesocosm representing Chezzetcook Inlet, a cool-temperate salt marsh in eastern Canada. We determined culture requirements for the agglutinated foraminifera in Petri dishes over 10–12 week periods. Five inexpensive, non-terminal ways of identifying live organisms were developed: spatial movement, detritus-gathering, attachment, clustering, and test opacity. Comparison with rose Bengal staining showed <10% diversion for calcareous species and T. inflata but M. fusca was over-counted by >30%. Terminal chambers of Trochammina inflata were examined by transmission electron microscopy to visualise food consumption and identify food in digestive vacuoles, both in specimens from mesocosm and in culture. Bacteria and unidentified detritus in the vacuoles establish that this agglutinated species is a saprophagous and bacterivorous detritivore. The adhesive secretions by these species apparently help them gather and possibly farm food while being relatively immobile in the sediments. Our observations of movement and feeding orientation in the agglutinants suggest links between form and function that underscore their value as ultra high resolution sea-level proxies. Mesocosm biomass and abundance counts show that foraminifera represent >50% of the meiofaunal biomass, emphasising their importance in the food web and energy-flow dynamics of temperate salt marsh systems.

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Distribution of Salt-marsh foraminifera in Jiaozhou Bay: Implications for sea-level reconstructions

10.5194/egusphere-egu2020-10354 ◽

2020 ◽

Author(s):

Haiyan Long ◽

Ziye Li

Keyword(s):

Salt Marsh ◽

Sea Level ◽

Environmental Changes ◽

Jiaozhou Bay ◽

The Yellow Sea ◽

Western Margin ◽

Latitude Range ◽

Tidal Salt Marsh ◽

Key Indicators ◽

Salt Marsh Species

Salt-marsh foraminifera are routinely used as sea-level indicators since their vertical distribution is closely linked with elevation relative to the tidal frame. In this study, 106 surface sediment samples were collected across separate intertidal transects established at five micro-tidal salt-marsh situated along the&#160;coasts of the Jiaozhou Bay, western margin of the Yellow Sea, dead and live foraminifera were identified respectively. The dead population contains the mixture of both subtidal species and salt-marsh species, and all the live assemblages consist of salt-marsh species which can provide exact information of salt-marsh foraminiferal distribution. The agglutinated species present in the five marshes including Trochammina inflata, Miliammina fusca and Jadammina macrecens are all cosmopolitan species, however, the calcareous species contain numbers of endemic species, overall, dominant calcareous species included Cribrononion porisuturalis, Pseudononionella variabilis, Elphidiella kiangsuensis and Pseudogyroidina sinensis. Vertical foraminifera zonations have been recognized in Daguhe and Hongshiya marsh samples with some species occupying strict latitude range, which primarily related to elevation, however, no obvious assemblages zonations can be recognized in Nvgukou, Shanjiaodi and Yanghe marsh. We hypothesize that salt-marsh foraminifera in Jiaozhou Bay possesses potential in paleoenvironmental studies as the key indicators for monitoring Holocene sea-level and environmental changes.

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Spatially-resolved correlative microscopy and microbial identification reveals dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment

10.1101/2020.08.03.234146 ◽

2020 ◽

Author(s):

Jeffrey Marlow ◽

Rachel Spietz ◽

Keun-Young Kim ◽

Mark Ellisman ◽

Peter Girguis ◽

...

Keyword(s):

Salt Marsh ◽

Microbial Communities ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Community Members ◽

Marsh Sediment ◽

Anabolic Activity ◽

Salt Marsh Sediment ◽

Rrna Gene Sequencing ◽

And Function

AbstractCoastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were embedded and analyzed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ∼60% in the top cm to 10-25% between 2-7 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase, and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.Statement of SignificanceMicroscale spatial relationships dictate critical aspects of a microbiome’s inner workings and emergent properties, such as evolutionary pathways, niche development, and community structure and function. However, many commonly used methods in microbial ecology neglect this parameter – obscuring important microbe-microbe and microbe-mineral interactions – and instead employ bulk-scale methodologies that are incapable of resolving these intricate relationships.This benchmark study presents a compelling new approach for exploring the anabolic activity of a complex microbial community by mapping the precise spatial configuration of anabolically active organisms within mineralogically heterogeneous sediment through in situ incubation, resin embedding, and correlative fluorescence and electron microscopy. In parallel, active organisms were identified through fluorescence-activated cell sorting and 16S rRNA gene sequencing, enabling a powerful interpretive framework connecting location, identity, activity, and putative biogeochemical roles of microbial community members.We deploy this novel approach in salt marsh sediment, revealing quantitative insights into the fundamental principles that govern the structure and function of sediment-hosted microbial communities. In particular, at different sediment horizons, we observed striking changes in the proportion of anabolically active cells, the identities of the most prominent active community members, and the nature of microbe-mineral affiliations. Improved approaches for understanding microscale ecosystems in a new light, such as those presented here, reveal environmental parameters that promote or constrain metabolic activity and clarify the impact that microbial communities have on our world.

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Anatomy of a selectively coassembled β-sheet peptide nanofiber

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1912810117 ◽

2020 ◽

Vol 117 (9) ◽

pp. 4710-4717 ◽

Cited By ~ 5

Author(s):

Qing Shao ◽

Kong M. Wong ◽

Dillon T. Seroski ◽

Yiming Wang ◽

Renjie Liu ◽

...

Keyword(s):

Self Assembly ◽

Molecular Level ◽

Form And Function ◽

Transmission Electron ◽

Peptide Pair ◽

High Concentrations ◽

Dynamics Simulations ◽

And Function ◽

20 Nm ◽

Β Sheet

Peptide self-assembly, wherein molecule A associates with other A molecules to form fibrillar β-sheet structures, is common in nature and widely used to fabricate synthetic biomaterials. Selective coassembly of peptide pairs A and B with complementary partial charges is gaining interest due to its potential for expanding the form and function of biomaterials that can be realized. It has been hypothesized that charge-complementary peptides organize into alternating ABAB-type arrangements within assembled β-sheets, but no direct molecular-level evidence exists to support this interpretation. We report a computational and experimental approach to characterize molecular-level organization of the established peptide pair, CATCH. Discontinuous molecular dynamics simulations predict that CATCH(+) and CATCH(−) peptides coassemble but do not self-assemble. Two-layer β-sheet amyloid structures predominate, but off-pathway β-barrel oligomers are also predicted. At low concentration, transmission electron microscopy and dynamic light scattering identified nonfibrillar ∼20-nm oligomers, while at high concentrations elongated fibers predominated. Thioflavin T fluorimetry estimates rapid and near-stoichiometric coassembly of CATCH(+) and CATCH(−) at concentrations ≥100 μM. Natural abundance13C NMR and isotope-edited Fourier transform infrared spectroscopy indicate that CATCH(+) and CATCH(−) coassemble into two-component nanofibers instead of self-sorting. However,13C–13C dipolar recoupling solid-state NMR measurements also identify nonnegligible AA and BB interactions among a majority of AB pairs. Collectively, these results demonstrate that strictly alternating arrangements of β-strands predominate in coassembled CATCH structures, but deviations from perfect alternation occur. Off-pathway β-barrel oligomers are also suggested to occur in coassembled β-strand peptide systems.

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Future sea-level rise drives rocky intertidal habitat loss and benthic community change

10.1101/553933 ◽

2019 ◽

Author(s):

Nikolas J. Kaplanis ◽

Clinton B. Edwards ◽

Yoan Eynaud ◽

Jennifer E. Smith

Keyword(s):

Sea Level Rise ◽

Sea Level ◽

Large Scale ◽

Environmental Changes ◽

Community Change ◽

Rocky Intertidal ◽

Spatially Explicit ◽

Benthic Habitat ◽

Large Area ◽

And Function

AbstractRocky intertidal ecosystems may be particularly susceptible to sea-level rise impacts but few studies have explored community scale response to future sea-level scenarios. Combining remote-sensing with large-area imaging, we quantify habitat extent and describe biological community structure at two rocky intertidal study locations in California. We then estimate changes in habitat area and community composition under a range of sea-level rise scenarios using a model-based approach. Our results suggest that future sea-level rise will significantly reduce rocky intertidal area at our study locations, leading to an overall decrease in benthic habitat and a reduction in overall invertebrate abundances, but increased densities of certain taxa. These results suggest that sea-level rise may fundamentally alter the structure and function of rocky intertidal systems. As large scale environmental changes such as sea-level rise accelerate in the next century, more extensive spatially-explicit monitoring at ecologically relevant scales will be needed to visualize and quantify the impacts to biological systems.

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Structure of contact sites between the outer and inner mitochondrial membranes investigated by HVEM tomography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100167299 ◽

1996 ◽

Vol 54 ◽

pp. 966-967

Author(s):

C.A. Mannella ◽

K.F. Buttle ◽

K.A. O‘Farrell ◽

A. Leith ◽

M. Marko

Keyword(s):

Liver Mitochondrion ◽

Adenine Nucleotide ◽

Protein Complexes ◽

Mitochondrial Membranes ◽

Electron Microscopic ◽

Contact Sites ◽

Transmission Electron ◽

Precursor Proteins ◽

Membrane Contacts ◽

And Function

Early transmission electron microscopy of plastic-embedded, thin-sectioned mitochondria indicated that there are numerous junctions between the outer and inner membranes of this organelle. More recent studies have suggested that the mitochondrial membrane contacts may be the site of protein complexes engaged in specialized functions, e.g., import of mitochondrial precursor proteins, adenine nucleotide channeling, and even intermembrane signalling. It has been suggested that the intermembrane contacts may be sites of membrane fusion involving non-bilayer lipid domains in the two membranes. However, despite growing interest in the nature and function of intramitochondrial contact sites, little is known about their structure.We are using electron microscopic tomography with the Albany HVEM to determine the internal organization of mitochondria. We have reconstructed a 0.6-μm section through an isolated, plasticembedded rat-liver mitochondrion by combining 123 projections collected by tilting (+/- 70°) around two perpendicular tilt axes. The resulting 3-D image has confirmed the basic inner-membrane organization inferred from lower-resolution reconstructions obtained from single-axis tomography.

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Scanning tunneling microscopy (STM) of DNA and RNA

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100152148 ◽

1989 ◽

Vol 47 ◽

pp. 34-35

Author(s):

Patricia G. Arscott ◽

Gil Lee ◽

Victor A. Bloomfield ◽

D. Fennell Evans

Keyword(s):

Molecular Structures ◽

Inorganic Materials ◽

Resolving Power ◽

Scanning Tunneling ◽

Tunneling Microscopy ◽

Form And Function ◽

Dna And Rna ◽

Calf Thymus ◽

And Function ◽

The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

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