Compound-specific 13 C stable isotope probing confirms synthesis of polyhydroxybutyrate by soil bacteria

Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients

Many microorganisms synthesise carbon (C)-rich compounds under resource deprivation. Such compounds likely serve as intracellular C-storage pools that sustain the activities of microorganisms growing on stoichiometrically imbalanced substrates, making them potentially vital to the function of ecosystems on infertile soils. We examined the dynamics and drivers of three putative C-storage compounds (neutral lipid fatty acids [NLFAs], polyhydroxybutyrate [PHB], and trehalose) across a natural gradient of soil fertility in eastern Australia. Together, NLFAs, PHB, and trehalose corresponded to 8.5-40% of microbial C and 0.06-0.6% of soil organic C. When scaled to "structural" microbial biomass (indexed by polar lipid fatty acids; PLFAs), NLFA and PHB allocation was 2-3-times greater in infertile soils derived from ironstone and sandstone than in comparatively fertile basalt- and shale-derived soils. PHB allocation was positively correlated with belowground biological phosphorus (P)-demand, while NLFA allocation was positively correlated with fungal PLFA : bacterial PLFA ratios. A complementary incubation revealed positive responses of respiration, storage, and fungal PLFAs to glucose, while bacterial PLFAs responded positively to PO43-. By comparing these results to a model of microbial C-allocation, we reason that NLFA primarily served the "reserve" storage mode for C-limited taxa (i.e., fungi), while the variable portion of PHB likely served as "surplus" C-storage for P-limited bacteria. Thus, our findings reveal a convergence of community-level processes (i.e., changes in taxonomic composition that underpin reserve-mode storage dynamics) and intracellular mechanisms (e.g., physiological plasticity of surplus-mode storage) that drives strong, predictable community-level microbial C-storage dynamics across gradients of soil fertility and substrate stoichiometry.

Intracellular carbon storage by microorganisms is an overlooked pathway of biomass growth

The concept of biomass growth is central to microbial carbon (C) cycling and ecosystem nutrient turnover. Microbial biomass is usually assumed to grow by cellular replication, despite microorganisms' capacity to increase biomass by synthesizing storage compounds. Resource investment in storage allows microbes to decouple their metabolic activity from immediate resource supply, supporting more diverse microbial responses to environmental changes. Here we show that microbial C storage in the form of triacylglycerides (TAGs) and polyhydroxybutyrate (PHB) contributes significantly to the formation of new biomass, i.e. growth, under contrasting conditions of C availability and complementary nutrient supply in soil. Together these compounds can comprise a C pool 0.19 ± 0.03 to 0.46 ± 0.08 times as large as extractable soil microbial biomass and reveal up to 279 ± 72% more biomass growth than observed by a DNA-based method alone. Even under C limitation, storage represented an additional 16-96% incorporation of added C into microbial biomass. These findings encourage greater recognition of storage synthesis as a key pathway of biomass growth and an underlying mechanism for resistance and resilience of microbial communities facing environmental change.

Effect of Polymer Properties on the Biodegradation of Polyurethane Microplastics

The release of fragments from plastic products, that is, secondary microplastics, is a major concern in the context of the global plastic pollution. Currently available (thermoplastic) polyurethanes [(T)PU] are not biodegradable and therefore should be recycled. However, the ester bond in (T)PUs might be sufficiently hydrolysable to enable at least partial biodegradation of polyurethane particles. Here, we investigated biodegradation in compost of different types of (T)PU to gain insights into their fragmentation and biodegradation mechanisms. The studied (T)PUs varied regarding the chemistry of their polymer backbone (aromatic/aliphatic), hard phase content, cross-linking degree, and presence of a hydrolysis-stabilizing additive. We developed and validated an efficient and non-destructive polymer particle extraction process for partially biodegraded (T)PUs based on ultrasonication and density separation. Our results showed that biodegradation rates and extents decreased with increasing cross-linking density and hard-segment content. We found that the presence of a hydrolysis stabilizer reduced (T)PU fragmentation while not affecting the conversion of (T)PU carbon into CO2. We propose a biodegradation mechanism for (T)PUs that includes both mother particle shrinkage by surface erosion and fragmentation. The presented results help to understand structure-degradation relationships of (T)PUs and support recycling strategies.

From energy to (soil organic) matter

In this concept paper, we propose a new view on soil organic matter (SOM) formation: microorganisms use most of the organics entering the soil as energy rather than as a source of carbon (C), while SOM accumulates as a residual by-product because the microbial energy investment in its decomposition exceeds the energy gain. During the initial stages of decomposition, the nominal oxidation state of C (NOSC) in remaining litter decreases, and the energy content increases. This reflects the rapid mineralization of available compounds with positive and neutral NOSC (carboxylic acids, sugars, some amino acids). Consequently, the NOSC of the remaining compounds drops to -0.3 units, and the oxidation rate decreases due to the residual relative accumulation of aromatic and aliphatic compounds (which are hydrolized later) and entombment of the necromass. Ultimately, incompletely decomposed plant residues will have 1%-2.5% more energy per C unit than the initial litter. The linear decrease in energy density of a broad range of organic substances by 106 kJ mol^-1 C per NOSC unit upon oxidation is supported by experimental data on litter decomposition. Preferential recycling of energy-rich reduced (lipids, aromatics, certain amino acids, amino sugars) and the microbial degradation of oxidized compounds (carboxylic acids) also energetically enrich SOM. Despite the high energy content, the availability of energy stored in SOM is lower than in litter. This explains why SOM is not fully mineralized (thermodynamically unfavorable), especially in the absence of plant C to provide new energy (e.g., in bare soil). Energy from litter activates decomposers to mine nutrients stored in SOM (the main ecological function of priming effects) because the nutrient content in SOM is 2-5 times higher than that of litter. This results in only 0.4%-5% year^-1 of litter-derived C being sequestered in SOM, whereas SOM stores 1%-10% year^-1 of the total litter-derived energy. Thus, the energy captured by photosynthesis is the main reason why microorganisms utilize organic matter, whereby SOM is merely a residual by-product of nutrient storage and a mediator of energy fluxes.

Microbial storage and its implications for soil ecology

Organisms throughout the tree of life accumulate chemical resources, in particular forms or compartments, to secure their availability for future use. Here we review microbial storage and its ecological significance by assembling several rich but disconnected lines of research in microbiology, biogeochemistry, and the ecology of macroscopic organisms. Evidence is drawn from various systems, but we pay particular attention to soils, where microorganisms play crucial roles in global element cycles. An assembly of genus-level data demonstrates the likely prevalence of storage traits in soil. We provide a theoretical basis for microbial storage ecology by distinguishing a spectrum of storage strategies ranging from surplus storage (storage of abundant resources that are not immediately required) to reserve storage (storage of limited resources at the cost of other metabolic functions). This distinction highlights that microorganisms can invest in storage at times of surplus and under conditions of scarcity. We then align storage with trait-based microbial life-history strategies, leading to the hypothesis that ruderal species, which are adapted to disturbance, rely less on storage than microorganisms adapted to stress or high competition. We explore the implications of storage for soil biogeochemistry, microbial biomass, and element transformations and present a process-based model of intracellular carbon storage. Our model indicates that storage can mitigate against stoichiometric imbalances, thereby enhancing biomass growth and resource-use efficiency in the face of unbalanced resources. Given the central roles of microbes in biogeochemical cycles, we propose that microbial storage may be influential on macroscopic scales, from carbon cycling to ecosystem stability.

Intracellular Storage Reduces Stoichiometric Imbalances in Soil Microbial Biomass – A Theoretical Exploration

Microbial intracellular storage is key to defining microbial resource use strategies and could contribute to carbon (C) and nutrient cycling. However, little attention has been devoted to the role of intracellular storage in soil processes, in particular from a theoretical perspective. Here we fill this gap by integrating intracellular storage dynamics into a microbially explicit soil C and nutrient cycling model. Two ecologically relevant modes of storage are considered: reserve storage, in which elements are routed to a storage compartment in proportion to their uptake rate, and surplus storage, in which elements in excess of microbial stoichiometric requirements are stored and limiting elements are remobilized from storage to fuel growth and microbial maintenance. Our aim is to explore with this model how these different storage modes affect the retention of C and nutrients in active microbial biomass under idealized conditions mimicking a substrate pulse experiment. As a case study, we describe C and phosphorus (P) dynamics using literature data to estimate model parameters. Both storage modes enhance the retention of elements in microbial biomass, but the surplus storage mode is more effective to selectively store or remobilize C and nutrients according to microbial needs. Enhancement of microbial growth by both storage modes is largest when the substrate C:nutrient ratio is high (causing nutrient limitation after substrate addition) and the amount of added substrate is large. Moreover, storage increases biomass nutrient retention and growth more effectively when resources are supplied in a few large pulses compared to several smaller pulses (mimicking a nearly constant supply), which suggests storage to be particularly relevant in highly dynamic soil microhabitats. Overall, our results indicate that storage dynamics are most important under conditions of strong stoichiometric imbalance and may be of high ecological relevance in soil environments experiencing large variations in C and nutrient supply.

Quantification of Synthetic Polyesters from Biodegradable Mulch Films in Soils

Soil biodegradable mulch films composed of the polyester polybutylene adipate-co-terephthalate (PBAT) are being increasingly used in agriculture. Analytical methods to quantify PBAT in field soils are needed to assess its soil occurrence and fate. Here, we report an analytical method for PBAT in soils that couples Soxhlet extraction or accelerated solvent extraction (ASE) with quantitative protonnuclear magnetic resonance (q-¹H NMR) spectroscopy detection. The ¹H NMR peak areas of aromatic PBAT protons increased linearly with PBAT concentrations dissolved in deuterated chloroform (CDCl₃), demonstrating accurate quantitation of PBAT by q-¹H NMR. Spike-recovery experiments involving PBAT addition to model sorbents and soils showed increased PBAT extraction efficiencies into chloroform (CHCl₃) with methanol (MeOH) as cosolvent, consistent with MeOH competitively displacing PBAT from H-bond donating sites on mineral surfaces. Systematic variations in solvent composition and temperatures in ASE revealed quantitative PBAT extraction from soil with 90/10 volume % CHCl₃/MeOH at 110-120 °C. Both Soxhlet extraction and ASE resulted in the complete recovery of PBAT added to a total of seven agricultural soils covering a range of physicochemical properties, independent of whether PBAT was added to soils dissolved in CHCl₃, as film, or as particles. Recovery was also complete for PBAT added to soil in the form of a commercial soil biodegradable mulch film with coextractable polylactic acid (PLA). The presented analytical method enables accurate quantification and biodegradation monitoring of PBAT in agricultural field soils.